=============================================================================== About this build: this rebuild has been done as part of reproduce.debian.net where we aim to reproduce Debian binary packages distributed via ftp.debian.org, by rebuilding using the exact same packages as the original build on the buildds, as described in the relevant .buildinfo file from buildinfos.debian.net. For more information please go to https://reproduce.debian.net or join #debian-reproducible on irc.debian.org =============================================================================== Preparing download of sources for /srv/rebuilderd/tmp/rebuilderdHqcnof/inputs/gromacs_2026.2-2_riscv64.buildinfo Source: gromacs Version: 2026.2-2 rebuilderd-worker node: riscv64-33 +------------------------------------------------------------------------------+ | Downloading sources Thu, 14 May 2026 23:03:54 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [140 kB] Get:2 https://deb.debian.org/debian-security trixie-security InRelease [43.4 kB] Get:3 https://deb.debian.org/debian trixie-updates InRelease [47.3 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [60.6 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [54.0 kB] Get:6 https://deb.debian.org/debian forky InRelease [151 kB] Get:7 https://deb.debian.org/debian sid InRelease [189 kB] Get:8 https://deb.debian.org/debian experimental InRelease [91.7 kB] Get:9 https://deb.debian.org/debian trixie/non-free-firmware Sources [6,552 B] Get:10 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:11 https://deb.debian.org/debian-security trixie-security/main Sources [150 kB] Get:12 https://deb.debian.org/debian-security trixie-security/non-free-firmware Sources [696 B] Get:13 https://deb.debian.org/debian trixie-updates/main Sources [2,788 B] Get:14 https://deb.debian.org/debian trixie-proposed-updates/main Sources [214 kB] Get:15 https://deb.debian.org/debian trixie-backports/main Sources [214 kB] Get:16 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [3,172 B] Get:17 https://deb.debian.org/debian forky/non-free-firmware Sources [8,488 B] Get:18 https://deb.debian.org/debian forky/main Sources [10.7 MB] Get:19 https://deb.debian.org/debian sid/non-free-firmware Sources [10.5 kB] Get:20 https://deb.debian.org/debian sid/main Sources [11.5 MB] Get:21 https://deb.debian.org/debian experimental/main Sources [429 kB] Get:22 https://deb.debian.org/debian experimental/non-free-firmware Sources [2,568 B] Fetched 34.5 MB in 34s (1,011 kB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.2-2.dsc' gromacs_2026.2-2.dsc 2814 SHA256:2dfe646b0d564c8800bb15f8a66b93f6bbec82ce1a8e67204c456afa7a978bdf 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.2.orig-regressiontests.tar.gz' gromacs_2026.2.orig-regressiontests.tar.gz 16580813 SHA256:f5fe50134d01e0c961812537cbb8253a4bd06831b6e329144ddbb6ba22393a36 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.2.orig.tar.gz' gromacs_2026.2.orig.tar.gz 45943914 SHA256:d27e4455e8246177952366798631a0dad9f2e1f567400a6cb854a168dcc050dd 'https://deb.debian.org/debian/pool/main/g/gromacs/gromacs_2026.2-2.debian.tar.xz' gromacs_2026.2-2.debian.tar.xz 13658756 SHA256:6ed2b4bea7dad0c87c0df14c99df6baa488c57ec196ce167f43729f1eb8ed1cb f5fe50134d01e0c961812537cbb8253a4bd06831b6e329144ddbb6ba22393a36 gromacs_2026.2.orig-regressiontests.tar.gz d27e4455e8246177952366798631a0dad9f2e1f567400a6cb854a168dcc050dd gromacs_2026.2.orig.tar.gz 6ed2b4bea7dad0c87c0df14c99df6baa488c57ec196ce167f43729f1eb8ed1cb gromacs_2026.2-2.debian.tar.xz 2dfe646b0d564c8800bb15f8a66b93f6bbec82ce1a8e67204c456afa7a978bdf gromacs_2026.2-2.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Thu, 14 May 2026 23:06:29 +0000 | +------------------------------------------------------------------------------+ + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdHqcnof/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdHqcnof/inputs/gromacs_2026.2-2_riscv64.buildinfo Rebuilding gromacs=2026.2-2 in /srv/rebuilderd/tmp/rebuilderdHqcnof/inputs now. /srv/rebuilderd/tmp/rebuilderdHqcnof/inputs/gromacs_2026.2-2_riscv64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/gromacs-2026.2 I: verifying dsc... successful! Get:1 http://deb.debian.org/debian unstable InRelease [189 kB] Get:2 http://snapshot.debian.org/archive/debian/20260514T022936Z forky InRelease [151 kB] Get:3 http://deb.debian.org/debian unstable/main riscv64 Packages [10.0 MB] Get:4 http://snapshot.debian.org/archive/debian/20260514T022936Z forky/main riscv64 Packages [9344 kB] Fetched 19.7 MB in 8s (2375 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20260514T022936Z/dists/forky/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://deb.debian.org/debian unstable/main riscv64 libjs-sphinxdoc all 9.1.0-3 [25.3 kB] Fetched 25.3 kB in 0s (1236 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk798fhd7/libjs-sphinxdoc_9.1.0-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libc6 riscv64 2.42-16 [1398 kB] Fetched 1398 kB in 0s (16.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp84ls6iaw/libc6_2.42-16_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3 riscv64 3.13.9-3+b1 [25.4 kB] Fetched 25.4 kB in 0s (1165 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1eu6bf7x/python3_3.13.9-3+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 cpp-riscv64-linux-gnu riscv64 4:15.2.0-5+b1 [4632 B] Fetched 4632 B in 0s (237 kB/s) dpkg-name: info: moved 'cpp-riscv64-linux-gnu_4%3a15.2.0-5+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpa4mlln58/cpp-riscv64-linux-gnu_15.2.0-5+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libedit2 riscv64 3.1-20251016-1+b1 [92.0 kB] Fetched 92.0 kB in 0s (4250 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgr0wqlne/libedit2_3.1-20251016-1+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libhwloc15 riscv64 2.13.0-2 [157 kB] Fetched 157 kB in 0s (2788 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptk32ez0r/libhwloc15_2.13.0-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpipeline1 riscv64 1.5.8-3 [48.2 kB] Fetched 48.2 kB in 0s (2309 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw8qzjyhi/libpipeline1_1.5.8-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libelf1t64 riscv64 0.195-1 [62.5 kB] Fetched 62.5 kB in 0s (2955 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptow5fabf/libelf1t64_0.195-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 tzdata all 2026b-1 [260 kB] Fetched 260 kB in 0s (10.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppb5e7wmh/tzdata_2026b-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libsframe3 riscv64 2.46-3 [85.9 kB] Fetched 85.9 kB in 0s (3972 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7vmjfz0n/libsframe3_2.46-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libfftw3-single3 riscv64 3.3.10-2+b2 [379 kB] Fetched 379 kB in 0s (13.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgymxfl8s/libfftw3-single3_3.3.10-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 bsdextrautils riscv64 2.42-6 [102 kB] Fetched 102 kB in 0s (1834 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj_9qmqml/bsdextrautils_2.42-6_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Fetched 60.0 kB in 0s (2870 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpas3xj09p/autotools-dev_20240727.1+nmu1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libgdbm6t64 riscv64 1.26-1+b2 [78.1 kB] Fetched 78.1 kB in 0s (3643 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgn8vbiea/libgdbm6t64_1.26-1+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libbinutils riscv64 2.46-3 [508 kB] Fetched 508 kB in 0s (16.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc09uhpzg/libbinutils_2.46-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libdebhelper-perl all 13.31 [75.7 kB] Fetched 75.7 kB in 0s (3531 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpju86544a/libdebhelper-perl_13.31_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libmount1 riscv64 2.42-6 [227 kB] Fetched 227 kB in 0s (9171 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp660yqbtj/libmount1_2.42-6_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libnuma-dev riscv64 2.0.19-1+b2 [74.1 kB] Fetched 74.1 kB in 0s (1364 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphb8yieqz/libnuma-dev_2.0.19-1+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 rpcsvc-proto riscv64 1.4.3-1+b2 [62.3 kB] Fetched 62.3 kB in 0s (2982 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeap9yqcv/rpcsvc-proto_1.4.3-1+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 liblzma5 riscv64 5.8.3-1 [334 kB] Fetched 334 kB in 0s (12.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx76nv5f6/liblzma5_5.8.3-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 g++ riscv64 4:15.2.0-5+b1 [1332 B] Fetched 1332 B in 0s (66.4 kB/s) dpkg-name: info: moved 'g++_4%3a15.2.0-5+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmp2l0zvuwc/g++_15.2.0-5+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 linux-libc-dev all 7.0.4-1 [1959 kB] Fetched 1959 kB in 0s (31.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpszr6hfok/linux-libc-dev_7.0.4-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpython3-stdlib riscv64 3.13.9-3+b1 [8348 B] Fetched 8348 B in 0s (420 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpidyixwac/libpython3-stdlib_3.13.9-3+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libgdbm-compat4t64 riscv64 1.26-1+b2 [52.1 kB] Fetched 52.1 kB in 0s (2522 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp351vowuv/libgdbm-compat4t64_1.26-1+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 liblapack-dev riscv64 3.12.1-7+b1 [12.0 MB] Fetched 12.0 MB in 1s (19.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcmj82_10/liblapack-dev_3.12.1-7+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libnghttp2-14 riscv64 1.69.0-1 [89.0 kB] Fetched 89.0 kB in 6s (15.1 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuf85vzgi/libnghttp2-14_1.69.0-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 mount riscv64 2.42-6 [169 kB] Fetched 169 kB in 2s (77.0 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7smykaic/mount_2.42-6_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libuchardet0 riscv64 0.0.8-2+b2 [68.8 kB] Fetched 68.8 kB in 4s (15.8 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmcjx1xxm/libuchardet0_0.0.8-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libtinfo6 riscv64 6.6+20251231-1+b1 [349 kB] Fetched 349 kB in 3s (121 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp76e51vr/libtinfo6_6.6+20251231-1+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpython3-dev riscv64 3.13.9-3+b1 [8584 B] Fetched 8584 B in 0s (431 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpastik3h3/libpython3-dev_3.13.9-3+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libaudit1 riscv64 1:4.1.2-1+b1 [58.7 kB] Fetched 58.7 kB in 0s (2756 kB/s) dpkg-name: info: moved 'libaudit1_1%3a4.1.2-1+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpszfk511k/libaudit1_4.1.2-1+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libboost1.90-dev riscv64 1.90.0-6 [11.3 MB] Fetched 11.3 MB in 1s (19.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp412wpxfp/libboost1.90-dev_1.90.0-6_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libkrb5support0 riscv64 1.22.1-2.1 [31.5 kB] Fetched 31.5 kB in 0s (1540 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa_huupzz/libkrb5support0_1.22.1-2.1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gettext riscv64 0.23.2-2 [1679 kB] Fetched 1679 kB in 0s (30.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp59rccjem/gettext_0.23.2-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libblas3 riscv64 3.12.1-7+b1 [123 kB] Fetched 123 kB in 0s (2232 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuctyoqzx/libblas3_3.12.1-7+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libxau6 riscv64 1:1.0.11-1+b2 [20.7 kB] Fetched 20.7 kB in 0s (386 kB/s) dpkg-name: info: moved 'libxau6_1%3a1.0.11-1+b2_riscv64.deb' to '/srv/rebuilderd/tmp/tmpgh44ds2r/libxau6_1.0.11-1+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libjsoncpp26 riscv64 1.9.7-2 [83.2 kB] Fetched 83.2 kB in 0s (3888 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl2jgjms5/libjsoncpp26_1.9.7-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 lsb-release all 12.1-2 [6072 B] Fetched 6072 B in 0s (116 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjnyf64_e/lsb-release_12.1-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libcrypt1 riscv64 1:4.5.1-1+b1 [113 kB] Fetched 113 kB in 0s (5069 kB/s) dpkg-name: info: moved 'libcrypt1_1%3a4.5.1-1+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpv8j3cvz5/libcrypt1_4.5.1-1+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 sed riscv64 4.9-3 [329 kB] Fetched 329 kB in 0s (12.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpklhwdfcb/sed_4.9-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gfortran-15-riscv64-linux-gnu riscv64 15.2.0-17 [15.3 MB] Fetched 15.3 MB in 0s (45.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1h5owdak/gfortran-15-riscv64-linux-gnu_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libevent-pthreads-2.1-7t64 riscv64 2.1.12-stable-10+b2 [54.1 kB] Fetched 54.1 kB in 0s (1006 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2kynbmdi/libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 binutils-riscv64-linux-gnu riscv64 2.46-3 [898 kB] Fetched 898 kB in 0s (23.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfqwrg26y/binutils-riscv64-linux-gnu_2.46-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libgmp10 riscv64 2:6.3.0+dfsg-5+b1 [563 kB] Fetched 563 kB in 0s (17.7 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-5+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpsqc39yyk/libgmp10_6.3.0+dfsg-5+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-numpy riscv64 1:2.4.4+ds-2 [4408 kB] Fetched 4408 kB in 0s (30.4 MB/s) dpkg-name: info: moved 'python3-numpy_1%3a2.4.4+ds-2_riscv64.deb' to '/srv/rebuilderd/tmp/tmp4ak5kua9/python3-numpy_2.4.4+ds-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 g++-riscv64-linux-gnu riscv64 4:15.2.0-5+b1 [1200 B] Fetched 1200 B in 0s (60.0 kB/s) dpkg-name: info: moved 'g++-riscv64-linux-gnu_4%3a15.2.0-5+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpme__l9p4/g++-riscv64-linux-gnu_15.2.0-5+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libsqlite3-0 riscv64 3.46.1-9+b1 [907 kB] Fetched 907 kB in 0s (22.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3nad8j5h/libsqlite3-0_3.46.1-9+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libuuid1 riscv64 2.42-6 [34.5 kB] Fetched 34.5 kB in 0s (1650 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzltw78cp/libuuid1_2.42-6_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 perl-base riscv64 5.40.1-7+b1 [1676 kB] Fetched 1676 kB in 0s (30.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpneoqq8xb/perl-base_5.40.1-7+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 autopoint all 0.23.2-2 [770 kB] Fetched 770 kB in 0s (21.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5mj3aa6v/autopoint_0.23.2-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libblkid1 riscv64 2.42-6 [192 kB] Fetched 192 kB in 0s (8004 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7uy_4snc/libblkid1_2.42-6_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-pluggy all 1.6.0-2 [27.2 kB] Fetched 27.2 kB in 0s (1318 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpslvqqi9j/python3-pluggy_1.6.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 automake all 1:1.18.1-4 [877 kB] Fetched 877 kB in 0s (22.6 MB/s) dpkg-name: info: moved 'automake_1%3a1.18.1-4_all.deb' to '/srv/rebuilderd/tmp/tmp_aa8ifup/automake_1.18.1-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpcre2-8-0 riscv64 10.46-1+b2 [296 kB] Fetched 296 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp5j16y3i/libpcre2-8-0_10.46-1+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 ncurses-base all 6.6+20251231-1 [277 kB] Fetched 277 kB in 0s (10.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuspoyyt_/ncurses-base_6.6+20251231-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3.13 riscv64 3.13.12-1 [776 kB] Fetched 776 kB in 0s (21.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpngso5nr_/python3.13_3.13.12-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gcc-15 riscv64 15.2.0-17 [531 kB] Fetched 531 kB in 0s (17.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp27zpcm4h/gcc-15_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 bash riscv64 5.3-3 [1560 kB] Fetched 1560 kB in 0s (29.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaj62ks7k/bash_5.3-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-networkx all 3.4.2-5 [23.9 MB] Fetched 23.9 MB in 1s (38.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpayj084i6/python3-networkx_3.4.2-5_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libmuparser-dev riscv64 2.3.4-2+b1 [33.5 kB] Fetched 33.5 kB in 0s (635 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2_mxk5ep/libmuparser-dev_2.3.4-2+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libbsd0 riscv64 0.12.2-2+b2 [132 kB] Fetched 132 kB in 0s (5811 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2jkahbwe/libbsd0_0.12.2-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libnl-3-dev riscv64 3.12.0-2+b1 [193 kB] Fetched 193 kB in 0s (3397 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp860cac2/libnl-3-dev_3.12.0-2+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libreadline8t64 riscv64 8.3-4 [180 kB] Fetched 180 kB in 0s (7434 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjvdn_row/libreadline8t64_8.3-4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libxdmcp6 riscv64 1:1.1.5-2+b1 [28.5 kB] Fetched 28.5 kB in 0s (1405 kB/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.5-2+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmp44eljro4/libxdmcp6_1.1.5-2+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 cmake riscv64 4.3.2-1 [15.2 MB] Fetched 15.2 MB in 0s (41.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvqw1ghih/cmake_4.3.2-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gfortran-15 riscv64 15.2.0-17 [20.8 kB] Fetched 20.8 kB in 0s (1020 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptxqr4ck8/gfortran-15_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libcc1-0 riscv64 16-20260425-1 [41.7 kB] Fetched 41.7 kB in 0s (2043 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphq3g9lpd/libcc1-0_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 bash-completion all 1:2.16.0-8 [319 kB] Fetched 319 kB in 0s (5415 kB/s) dpkg-name: info: moved 'bash-completion_1%3a2.16.0-8_all.deb' to '/srv/rebuilderd/tmp/tmpk1d6axck/bash-completion_2.16.0-8_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 perl-modules-5.40 all 5.40.1-7 [3012 kB] Fetched 3012 kB in 0s (25.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgznji2e4/perl-modules-5.40_5.40.1-7_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 findutils riscv64 4.10.0-4 [704 kB] Fetched 704 kB in 0s (20.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfrdugwuc/findutils_4.10.0-4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-iniconfig all 2.1.0-2 [7540 B] Fetched 7540 B in 0s (381 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp12764_hh/python3-iniconfig_2.1.0-2_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-pygments all 2.19.2+dfsg-1 [847 kB] Fetched 847 kB in 0s (22.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_u8i97l7/python3-pygments_2.19.2+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libbrotli1 riscv64 1.2.0-3 [357 kB] Fetched 357 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppizt9m4o/libbrotli1_1.2.0-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libprrte-bin riscv64 3.0.13-3 [50.8 kB] Fetched 50.8 kB in 0s (951 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgg78yp1s/libprrte-bin_3.0.13-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libexpat1 riscv64 2.8.0-2 [113 kB] Fetched 113 kB in 0s (5128 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu1s4ji68/libexpat1_2.8.0-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libprrte3 riscv64 3.0.13-3 [441 kB] Fetched 441 kB in 0s (7032 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgdlt3r8g/libprrte3_3.0.13-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libxml2-16 riscv64 2.15.2+dfsg-0.1 [639 kB] Fetched 639 kB in 0s (19.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwudsjpov/libxml2-16_2.15.2+dfsg-0.1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 cpp riscv64 4:15.2.0-5+b1 [1568 B] Fetched 1568 B in 0s (77.8 kB/s) dpkg-name: info: moved 'cpp_4%3a15.2.0-5+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmp2_kpzi6u/cpp_15.2.0-5+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 m4 riscv64 1.4.21-1 [330 kB] Fetched 330 kB in 0s (12.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp14zb3bfj/m4_1.4.21-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3.13-dev riscv64 3.13.12-1 [512 kB] Fetched 512 kB in 0s (8089 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1nhebaxr/python3.13-dev_3.13.12-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libfuse3-4 riscv64 3.18.2-2 [99.7 kB] Fetched 99.7 kB in 0s (1836 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa97xj3w6/libfuse3-4_3.18.2-2_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260514T022936Z forky/main riscv64 libpam0g riscv64 1.7.0-5+b1 [70.7 kB] Fetched 70.7 kB in 0s (1299 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsfqprr_v/libpam0g_1.7.0-5+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libuv1t64 riscv64 1.51.0-2+b2 [155 kB] Fetched 155 kB in 0s (6698 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn3w9z86g/libuv1t64_1.51.0-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libfido2-1 riscv64 1.17.0-1 [84.4 kB] Fetched 84.4 kB in 0s (3961 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqm8vlv1c/libfido2-1_1.17.0-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libisl23 riscv64 0.27-2 [662 kB] Fetched 662 kB in 0s (19.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnjvz1ijg/libisl23_0.27-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 coreutils riscv64 9.10-1 [3128 kB] Fetched 3128 kB in 0s (25.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3ix2kp1s/coreutils_9.10-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libnl-route-3-200 riscv64 3.12.0-2+b1 [200 kB] Fetched 200 kB in 0s (3499 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp85kcbcy8/libnl-route-3-200_3.12.0-2+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libldap2 riscv64 2.6.10+dfsg-1+b1 [196 kB] Fetched 196 kB in 0s (3438 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwmej9jh0/libldap2_2.6.10+dfsg-1+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 g++-15-riscv64-linux-gnu riscv64 15.2.0-17 [15.9 MB] Fetched 15.9 MB in 0s (43.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl7kmb_ka/g++-15-riscv64-linux-gnu_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 dash riscv64 0.5.12-12 [101 kB] Fetched 101 kB in 0s (4635 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvt6ggkv1/dash_0.5.12-12_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 mpi-default-bin riscv64 1.20 [2724 B] Fetched 2724 B in 0s (52.3 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0n7yrbpf/mpi-default-bin_1.20_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Fetched 319 kB in 0s (5398 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq52ab36h/libjs-jquery_3.7.1+dfsg+~3.5.33-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libnghttp3-9 riscv64 1.15.0-1 [66.9 kB] Fetched 66.9 kB in 0s (3152 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqhycvnpq/libnghttp3-9_1.15.0-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 pkgconf-bin riscv64 2.5.1-4 [35.1 kB] Fetched 35.1 kB in 0s (1706 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgab34pzk/pkgconf-bin_2.5.1-4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libucx0 riscv64 1.20.1~rc2-1 [909 kB] Fetched 909 kB in 0s (12.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb5pm7bzt/libucx0_1.20.1~rc2-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libtsan2 riscv64 16-20260425-1 [2705 kB] Fetched 2705 kB in 0s (35.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqjuxpjl8/libtsan2_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-minimal riscv64 3.13.9-3+b1 [25.4 kB] Fetched 25.4 kB in 0s (1230 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_6xmtvep/python3-minimal_3.13.9-3+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libubsan1 riscv64 16-20260425-1 [1191 kB] Fetched 1191 kB in 0s (26.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwv0rm1tv/libubsan1_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3.13-minimal riscv64 3.13.12-1 [2172 kB] Fetched 2172 kB in 0s (21.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ix83eb2/python3.13-minimal_3.13.12-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 base-passwd riscv64 3.6.8 [54.8 kB] Fetched 54.8 kB in 0s (2652 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcc0ucfhu/base-passwd_3.6.8_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 dwz riscv64 0.16-4 [115 kB] Fetched 115 kB in 0s (5165 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9okk_t_u/dwz_0.16-4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 debconf all 1.5.92 [123 kB] Fetched 123 kB in 0s (5487 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph16um83r/debconf_1.5.92_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libboost-dev riscv64 1.90.0.2 [3068 B] Fetched 3068 B in 0s (58.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo9gmivss/libboost-dev_1.90.0.2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libgfortran5 riscv64 16-20260425-1 [418 kB] Fetched 418 kB in 0s (14.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_o2xxa4d/libgfortran5_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libmunge2 riscv64 0.5.18-1 [19.1 kB] Fetched 19.1 kB in 0s (365 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpufspay3b/libmunge2_0.5.18-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libevent-core-2.1-7t64 riscv64 2.1.12-stable-10+b2 [133 kB] Fetched 133 kB in 0s (2405 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvh6vx2f2/libevent-core-2.1-7t64_2.1.12-stable-10+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libgprofng0 riscv64 2.46-3 [722 kB] Fetched 722 kB in 0s (20.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkiqo_8wr/libgprofng0_2.46-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpciaccess0 riscv64 0.17-3+b4 [51.4 kB] Fetched 51.4 kB in 0s (2452 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprcm0ppu0/libpciaccess0_0.17-3+b4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libx11-6 riscv64 2:1.8.13-1 [821 kB] Fetched 821 kB in 0s (22.1 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.13-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpobmpj1ie/libx11-6_1.8.13-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 openssl-provider-legacy riscv64 3.6.2-1 [318 kB] Fetched 318 kB in 0s (12.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_7b8kaze/openssl-provider-legacy_3.6.2-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 man-db riscv64 2.13.1-1 [1458 kB] Fetched 1458 kB in 0s (28.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptfr9fl6w/man-db_2.13.1-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-dev riscv64 3.13.9-3+b1 [29.8 kB] Fetched 29.8 kB in 0s (566 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpex_6rsv3/python3-dev_3.13.9-3+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libidn2-0 riscv64 2.3.8-5 [108 kB] Fetched 108 kB in 0s (4919 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpob3osic7/libidn2-0_2.3.8-5_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 librhash1 riscv64 1.4.6-1.1+b1 [143 kB] Fetched 143 kB in 0s (6210 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcteg9lpx/librhash1_1.4.6-1.1+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libxcb1 riscv64 1.17.0-2+b2 [145 kB] Fetched 145 kB in 0s (6314 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb1ek9vxu/libxcb1_1.17.0-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libxxhash0 riscv64 0.8.3-2+b2 [39.6 kB] Fetched 39.6 kB in 0s (1948 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmgtu2sm_/libxxhash0_0.8.3-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 xz-utils riscv64 5.8.3-1 [739 kB] Fetched 739 kB in 0s (10.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2uffw6rs/xz-utils_5.8.3-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libacl1 riscv64 2.3.2-3 [32.7 kB] Fetched 32.7 kB in 0s (1592 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0arfh_rs/libacl1_2.3.2-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libhwloc-plugins riscv64 2.13.0-2 [17.8 kB] Fetched 17.8 kB in 0s (341 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0nd9tk6b/libhwloc-plugins_2.13.0-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gcc-15-riscv64-linux-gnu riscv64 15.2.0-17 [28.9 MB] Fetched 28.9 MB in 1s (43.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq0a9a7bu/gcc-15-riscv64-linux-gnu_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libudev1 riscv64 260.1-1 [134 kB] Fetched 134 kB in 0s (5921 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp505emu8b/libudev1_260.1-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libstdc++6 riscv64 16-20260425-1 [776 kB] Fetched 776 kB in 0s (11.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9n1_whs1/libstdc++6_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 mawk riscv64 1.3.4.20260302-1 [142 kB] Fetched 142 kB in 0s (6201 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5nanqii5/mawk_1.3.4.20260302-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 dh-autoreconf all 22 [12.2 kB] Fetched 12.2 kB in 0s (598 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp19ei4ne4/dh-autoreconf_22_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 po-debconf all 1.0.22 [216 kB] Fetched 216 kB in 0s (8920 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_jc6ed_n/po-debconf_1.0.22_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libperl5.40 riscv64 5.40.1-7+b1 [3958 kB] Fetched 3958 kB in 0s (38.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu7gzw8ji/libperl5.40_5.40.1-7+b1_riscv64.deb' Downloading dependency 1 of 281: libjs-sphinxdoc:riscv64=9.1.0-3 Downloading dependency 2 of 281: libc6:riscv64=2.42-16 Downloading dependency 3 of 281: python3:riscv64=3.13.9-3+b1 Downloading dependency 4 of 281: cpp-riscv64-linux-gnu:riscv64=4:15.2.0-5+b1 Downloading dependency 5 of 281: libedit2:riscv64=3.1-20251016-1+b1 Downloading dependency 6 of 281: libhwloc15:riscv64=2.13.0-2 Downloading dependency 7 of 281: libpipeline1:riscv64=1.5.8-3 Downloading dependency 8 of 281: libelf1t64:riscv64=0.195-1 Downloading dependency 9 of 281: tzdata:riscv64=2026b-1 Downloading dependency 10 of 281: libsframe3:riscv64=2.46-3 Downloading dependency 11 of 281: libfftw3-single3:riscv64=3.3.10-2+b2 Downloading dependency 12 of 281: bsdextrautils:riscv64=2.42-6 Downloading dependency 13 of 281: autotools-dev:riscv64=20240727.1+nmu1 Downloading dependency 14 of 281: libgdbm6t64:riscv64=1.26-1+b2 Downloading dependency 15 of 281: libbinutils:riscv64=2.46-3 Downloading dependency 16 of 281: libdebhelper-perl:riscv64=13.31 Downloading dependency 17 of 281: libmount1:riscv64=2.42-6 Downloading dependency 18 of 281: libnuma-dev:riscv64=2.0.19-1+b2 Downloading dependency 19 of 281: rpcsvc-proto:riscv64=1.4.3-1+b2 Downloading dependency 20 of 281: liblzma5:riscv64=5.8.3-1 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http://snapshot.debian.org/archive/debian/20260514T022936Z forky/main riscv64 autoconf all 2.72-6 [494 kB] Fetched 494 kB in 0s (16.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0u6x1ukp/autoconf_2.72-6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260514T022936Z forky/main riscv64 base-files riscv64 14 [72.9 kB] Fetched 72.9 kB in 0s (2633 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8k43_1jh/base-files_14_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libgcc-15-dev riscv64 15.2.0-17 [5649 kB] Fetched 5649 kB in 0s (41.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6ui870wj/libgcc-15-dev_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libgcc-s1 riscv64 16-20260425-1 [74.2 kB] Fetched 74.2 kB in 0s (3484 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpobm5piky/libgcc-s1_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libngtcp2-crypto-ossl0 riscv64 1.22.1-1 [23.5 kB] Fetched 23.5 kB in 0s (1170 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0d81r5zf/libngtcp2-crypto-ossl0_1.22.1-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 ibverbs-providers riscv64 63.0-1 [402 kB] Fetched 402 kB in 0s (6626 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyy98oeyo/ibverbs-providers_63.0-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libevent-dev riscv64 2.1.12-stable-10+b2 [571 kB] Fetched 571 kB in 0s (8866 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5dnmknc6/libevent-dev_2.1.12-stable-10+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-numpy-dev riscv64 1:2.4.4+ds-2 [183 kB] Fetched 183 kB in 0s (3210 kB/s) dpkg-name: info: moved 'python3-numpy-dev_1%3a2.4.4+ds-2_riscv64.deb' to '/srv/rebuilderd/tmp/tmp4go687dl/python3-numpy-dev_2.4.4+ds-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 dh-python all 7.20260309 [114 kB] Fetched 114 kB in 0s (5168 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz5redjkr/dh-python_7.20260309_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260514T022936Z forky/main riscv64 libpam-modules riscv64 1.7.0-5+b1 [176 kB] Fetched 176 kB in 0s (7504 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4l872spo/libpam-modules_1.7.0-5+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libfftw3-double3 riscv64 3.3.10-2+b2 [376 kB] Fetched 376 kB in 0s (13.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpukv__ec3/libfftw3-double3_3.3.10-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libltdl7 riscv64 2.5.4-11 [415 kB] Fetched 415 kB in 0s (14.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyy2pb144/libltdl7_2.5.4-11_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libmagic-mgc riscv64 1:5.46-5+b2 [337 kB] Fetched 337 kB in 0s (12.4 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-5+b2_riscv64.deb' to '/srv/rebuilderd/tmp/tmp1q4wcki2/libmagic-mgc_5.46-5+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libmuparser2v5 riscv64 2.3.4-2+b1 [144 kB] Fetched 144 kB in 0s (2547 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfblf72mu/libmuparser2v5_2.3.4-2+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 patch riscv64 2.8-2 [134 kB] Fetched 134 kB in 0s (5994 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptg4mtuq2/patch_2.8-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 grep riscv64 3.12-1 [442 kB] Fetched 442 kB in 0s (15.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5_mlpz5j/grep_3.12-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libgssapi-krb5-2 riscv64 1.22.1-2.1 [139 kB] Fetched 139 kB in 0s (6109 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4vrv56jh/libgssapi-krb5-2_1.22.1-2.1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libitm1 riscv64 16-20260425-1 [25.5 kB] Fetched 25.5 kB in 0s (1270 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6a0igo4e/libitm1_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 zlib1g-dev riscv64 1:1.3.dfsg+really1.3.2-3 [991 kB] Fetched 991 kB in 0s (24.0 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.2-3_riscv64.deb' to '/srv/rebuilderd/tmp/tmpj82jybp3/zlib1g-dev_1.3.dfsg+really1.3.2-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpam-runtime all 1.7.0-5 [249 kB] Fetched 249 kB in 0s (9891 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9xyua3kx/libpam-runtime_1.7.0-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260514T022936Z forky/main riscv64 libcurl4t64 riscv64 8.20.0-1 [413 kB] Fetched 413 kB in 0s (14.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw0ahf9r7/libcurl4t64_8.20.0-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libatomic1 riscv64 16-20260425-1 [8536 B] Fetched 8536 B in 0s (433 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr0f3bv9w/libatomic1_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libkrb5-3 riscv64 1.22.1-2.1 [344 kB] Fetched 344 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_sd4g7uz/libkrb5-3_1.22.1-2.1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libssl3t64 riscv64 3.6.2-1 [2250 kB] Fetched 2250 kB in 0s (33.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp37al7csb/libssl3t64_3.6.2-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 file riscv64 1:5.46-5+b2 [42.4 kB] Fetched 42.4 kB in 0s (2055 kB/s) dpkg-name: info: moved 'file_1%3a5.46-5+b2_riscv64.deb' to '/srv/rebuilderd/tmp/tmp366cuc5u/file_5.46-5+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libcbor0.10 riscv64 0.10.2-2.1+b1 [27.5 kB] Fetched 27.5 kB in 0s (514 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo4a5pq1s/libcbor0.10_0.10.2-2.1+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libunistring5 riscv64 1.4.2-1 [475 kB] Fetched 475 kB in 0s (15.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy913n5jp/libunistring5_1.4.2-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gcc-riscv64-linux-gnu riscv64 4:15.2.0-5+b1 [1432 B] Fetched 1432 B in 0s (73.5 kB/s) dpkg-name: info: moved 'gcc-riscv64-linux-gnu_4%3a15.2.0-5+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmps6fnbad9/gcc-riscv64-linux-gnu_15.2.0-5+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libsystemd-shared riscv64 260.1-1 [2364 kB] Fetched 2364 kB in 0s (34.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdz71rrcu/libsystemd-shared_260.1-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 groff-base riscv64 1.24.1-1 [1311 kB] Fetched 1311 kB in 0s (27.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplxnbhj45/groff-base_1.24.1-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 zlib1g riscv64 1:1.3.dfsg+really1.3.2-3 [87.3 kB] Fetched 87.3 kB in 0s (3962 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.2-3_riscv64.deb' to '/srv/rebuilderd/tmp/tmpjrtoqreq/zlib1g_1.3.dfsg+really1.3.2-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libnl-3-200 riscv64 3.12.0-2+b1 [61.8 kB] Fetched 61.8 kB in 0s (1143 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2smua7eg/libnl-3-200_3.12.0-2+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gettext-base riscv64 0.23.2-2 [242 kB] Fetched 242 kB in 0s (9500 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp6e_x260/gettext-base_0.23.2-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 liblsan0 riscv64 16-20260425-1 [1342 kB] Fetched 1342 kB in 0s (27.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqzrf19pw/liblsan0_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libibverbs-dev riscv64 63.0-1 [1891 kB] Fetched 1891 kB in 0s (20.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphvnmg0qh/libibverbs-dev_63.0-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpython3.13-minimal riscv64 3.13.12-1 [862 kB] Fetched 862 kB in 0s (22.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp26io5ffv/libpython3.13-minimal_3.13.12-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gcc-15-base riscv64 15.2.0-17 [36.8 kB] Fetched 36.8 kB in 0s (1802 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5cjknsqp/gcc-15-base_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 ncurses-bin riscv64 6.6+20251231-1+b1 [439 kB] Fetched 439 kB in 0s (6941 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplx4fe6kz/ncurses-bin_6.6+20251231-1+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 sysvinit-utils riscv64 3.18-1 [29.3 kB] Fetched 29.3 kB in 0s (1448 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0hclgrdj/sysvinit-utils_3.18-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 binutils-common riscv64 2.46-3 [2632 kB] Fetched 2632 kB in 0s (34.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppacy4oit/binutils-common_2.46-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libopenmpi40 riscv64 5.0.10-1 [1924 kB] Fetched 1924 kB in 0s (18.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4sqrftcd/libopenmpi40_5.0.10-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libkeyutils1 riscv64 1.6.3-6+b2 [9256 B] Fetched 9256 B in 0s (455 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiitys0hm/libkeyutils1_1.6.3-6+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gcc-16-base riscv64 16-20260425-1 [35.8 kB] Fetched 35.8 kB in 0s (1767 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsrm9b6u7/gcc-16-base_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libsystemd0 riscv64 260.1-1 [456 kB] Fetched 456 kB in 0s (15.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjebxvyse/libsystemd0_260.1-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Fetched 8812 B in 0s (423 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_06e7asi/dh-strip-nondeterminism_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libevent-extra-2.1-7t64 riscv64 2.1.12-stable-10+b2 [108 kB] Fetched 108 kB in 0s (1969 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppbfgi8e7/libevent-extra-2.1-7t64_2.1.12-stable-10+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 mpi-default-dev riscv64 1.20 [3504 B] Fetched 3504 B in 0s (67.5 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvlk6hdb2/mpi-default-dev_1.20_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 openmpi-common all 5.0.10-1 [30.3 kB] Fetched 30.3 kB in 0s (572 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcit869fc/openmpi-common_5.0.10-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 architecture-properties riscv64 0.2.6+b2 [2636 B] Fetched 2636 B in 0s (47.5 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpojyp_vp3/architecture-properties_0.2.6+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 dpkg riscv64 1.23.7 [1534 kB] Fetched 1534 kB in 0s (18.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp06gibzeh/dpkg_1.23.7_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 perl riscv64 5.40.1-7+b1 [264 kB] Fetched 264 kB in 0s (10.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7wj3mkgr/perl_5.40.1-7+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpkgconf7 riscv64 2.5.1-4 [47.1 kB] Fetched 47.1 kB in 0s (2301 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpptku1268/libpkgconf7_2.5.1-4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libasan8 riscv64 16-20260425-1 [2993 kB] Fetched 2993 kB in 0s (35.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5rqquadk/libasan8_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libevent-openssl-2.1-7t64 riscv64 2.1.12-stable-10+b2 [60.6 kB] Fetched 60.6 kB in 0s (1131 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplxox0jh6/libevent-openssl-2.1-7t64_2.1.12-stable-10+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 util-linux riscv64 2.42-6 [1217 kB] Fetched 1217 kB in 0s (26.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsh2n7y60/util-linux_2.42-6_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 liblapack3 riscv64 3.12.1-7+b1 [1971 kB] Fetched 1971 kB in 0s (20.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ilfizyh/liblapack3_3.12.1-7+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libmpfr6 riscv64 4.2.2-3 [666 kB] Fetched 666 kB in 0s (19.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8z60if1e/libmpfr6_4.2.2-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpython3.13 riscv64 3.13.12-1 [2175 kB] Fetched 2175 kB in 0s (22.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo_8cmpm1/libpython3.13_3.13.12-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libucc1 riscv64 1.7.0~rc1-1 [304 kB] Fetched 304 kB in 0s (5142 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpin25tukt/libucc1_1.7.0~rc1-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libexpat1-dev riscv64 2.8.0-2 [344 kB] Fetched 344 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiui1avz8/libexpat1-dev_2.8.0-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libzstd1 riscv64 1.5.7+dfsg-3+b2 [368 kB] Fetched 368 kB in 0s (13.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps348h7p1/libzstd1_1.5.7+dfsg-3+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 dpkg-dev all 1.23.7 [1318 kB] Fetched 1318 kB in 0s (27.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpojygr2yo/dpkg-dev_1.23.7_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 sensible-utils all 0.0.26 [27.0 kB] Fetched 27.0 kB in 0s (1324 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzzw6pdf_/sensible-utils_0.0.26_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libsasl2-modules-db riscv64 2.1.28+dfsg1-11 [17.5 kB] Fetched 17.5 kB in 0s (879 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4aettbp8/libsasl2-modules-db_2.1.28+dfsg1-11_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libc6-dev riscv64 2.42-16 [3417 kB] Fetched 3417 kB in 0s (36.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp30hp2sv3/libc6-dev_2.42-16_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 cpp-15 riscv64 15.2.0-17 [1276 B] Fetched 1276 B in 0s (65.0 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9qgvwr9e/cpp-15_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 tar riscv64 1.35+dfsg-4 [821 kB] Fetched 821 kB in 0s (20.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsqwja89o/tar_1.35+dfsg-4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 build-essential riscv64 12.12 [4628 B] Fetched 4628 B in 0s (233 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzk80757c/build-essential_12.12_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libblas-dev riscv64 3.12.1-7+b1 [291 kB] Fetched 291 kB in 0s (4957 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3u0lf_7b/libblas-dev_3.12.1-7+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libarchive13t64 riscv64 3.8.7-1 [375 kB] Fetched 375 kB in 0s (13.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6mzf105e/libarchive13t64_3.8.7-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libcom-err2 riscv64 1.47.4-1 [18.9 kB] Fetched 18.9 kB in 0s (928 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw758u_c1/libcom-err2_1.47.4-1_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260514T022936Z forky/main riscv64 libpam-modules-bin riscv64 1.7.0-5+b1 [49.6 kB] Fetched 49.6 kB in 0s (2416 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuldz4zt3/libpam-modules-bin_1.7.0-5+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libdb5.3t64 riscv64 5.3.28+dfsg2-11+b1 [719 kB] Fetched 719 kB in 0s (20.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ncpuzhc/libdb5.3t64_5.3.28+dfsg2-11+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libgomp1 riscv64 16-20260425-1 [137 kB] Fetched 137 kB in 0s (5823 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc8dzethr/libgomp1_16-20260425-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libprrte-dev riscv64 3.0.13-3 [4586 kB] Fetched 4586 kB in 0s (29.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa3bsvgfa/libprrte-dev_3.0.13-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-packaging all 26.0-1 [64.3 kB] Fetched 64.3 kB in 0s (3026 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfnxhsteo/python3-packaging_26.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpython3.13-dev riscv64 3.13.12-1 [16.7 MB] Fetched 16.7 MB in 1s (20.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7h4mxcsn/libpython3.13-dev_3.13.12-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 make riscv64 4.4.1-3 [463 kB] Fetched 463 kB in 0s (15.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp47rqju75/make_4.4.1-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 g++-15 riscv64 15.2.0-17 [28.0 kB] Fetched 28.0 kB in 0s (1364 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw2ao5pz5/g++-15_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 media-types all 14.0.0 [30.8 kB] Fetched 30.8 kB in 0s (1517 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv8t7krl8/media-types_14.0.0_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Fetched 19.9 kB in 0s (1001 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfvnni4ir/libfile-stripnondeterminism-perl_1.15.0-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libc-bin riscv64 2.42-16 [586 kB] Fetched 586 kB in 0s (18.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpddctm32y/libc-bin_2.42-16_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 openssh-client riscv64 1:10.3p1-2 [983 kB] Fetched 983 kB in 0s (11.9 MB/s) dpkg-name: info: moved 'openssh-client_1%3a10.3p1-2_riscv64.deb' to '/srv/rebuilderd/tmp/tmp9li_43v_/openssh-client_10.3p1-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 debianutils riscv64 5.23.2 [91.7 kB] Fetched 91.7 kB in 0s (4126 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvl_499sg/debianutils_5.23.2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libnuma1 riscv64 2.0.19-1+b2 [22.8 kB] Fetched 22.8 kB in 0s (433 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy_mc5ya9/libnuma1_2.0.19-1+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 cpp-15-riscv64-linux-gnu riscv64 15.2.0-17 [14.8 MB] Fetched 14.8 MB in 0s (36.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpophikwkh/cpp-15-riscv64-linux-gnu_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libevent-2.1-7t64 riscv64 2.1.12-stable-10+b2 [183 kB] Fetched 183 kB in 0s (7643 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_7gg0skp/libevent-2.1-7t64_2.1.12-stable-10+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libibumad3 riscv64 63.0-1 [28.1 kB] Fetched 28.1 kB in 0s (522 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl6kvqldq/libibumad3_63.0-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 bzip2 riscv64 1.0.8-6+b2 [40.2 kB] Fetched 40.2 kB in 0s (1952 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzd3j6daf/bzip2_1.0.8-6+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpsl5t64 riscv64 0.21.5-1 [59.9 kB] Fetched 59.9 kB in 0s (2843 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxyi8teh5/libpsl5t64_0.21.5-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libstdc++-15-dev riscv64 15.2.0-17 [6743 kB] Fetched 6743 kB in 0s (42.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppu59m4k5/libstdc++-15-dev_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 librdmacm1t64 riscv64 63.0-1 [73.5 kB] Fetched 73.5 kB in 0s (1347 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf0496s8t/librdmacm1t64_63.0-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 openmpi-bin riscv64 5.0.10-1 [157 kB] Fetched 157 kB in 0s (2804 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmwopug1q/openmpi-bin_5.0.10-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 liblz4-1 riscv64 1.10.0-10 [86.3 kB] Fetched 86.3 kB in 0s (4000 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmc1mf901/liblz4-1_1.10.0-10_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libfabric1 riscv64 2.1.0-1.1+b2 [600 kB] Fetched 600 kB in 0s (9123 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5v0237xj/libfabric1_2.1.0-1.1+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libtool all 2.5.4-11 [539 kB] Fetched 539 kB in 0s (17.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphut1451y/libtool_2.5.4-11_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libopenmpi-dev riscv64 5.0.10-1 [1029 kB] Fetched 1029 kB in 0s (12.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl75dgpqv/libopenmpi-dev_5.0.10-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 procps riscv64 2:4.0.4-9+b2 [876 kB] Fetched 876 kB in 0s (22.7 MB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-9+b2_riscv64.deb' to '/srv/rebuilderd/tmp/tmpd6dpcie3/procps_4.0.4-9+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libx11-data all 2:1.8.13-1 [346 kB] Fetched 346 kB in 0s (12.7 MB/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.13-1_all.deb' to '/srv/rebuilderd/tmp/tmp8cpes01v/libx11-data_1.8.13-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gzip riscv64 1.13-1 [139 kB] Fetched 139 kB in 0s (6066 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9vlb3ba4/gzip_1.13-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libibmad5 riscv64 63.0-1 [43.1 kB] Fetched 43.1 kB in 0s (805 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpglb_rr4e/libibmad5_63.0-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libcap-ng0 riscv64 0.9.3-1 [17.5 kB] Fetched 17.5 kB in 0s (881 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5_t3586k/libcap-ng0_0.9.3-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libmpc3 riscv64 1.3.1-3 [56.5 kB] Fetched 56.5 kB in 0s (2727 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoi7l01sf/libmpc3_1.3.1-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 pybind11-dev all 3.0.1-3 [240 kB] Fetched 240 kB in 0s (4164 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3tkus_xb/pybind11-dev_3.0.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 hostname riscv64 3.25 [10.7 kB] Fetched 10.7 kB in 0s (540 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpywsm08fe/hostname_3.25_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 ocl-icd-libopencl1 riscv64 2.3.4-1+b1 [42.1 kB] Fetched 42.1 kB in 0s (2044 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyzcg5h0m/ocl-icd-libopencl1_2.3.4-1+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 netbase all 6.5 [12.4 kB] Fetched 12.4 kB in 0s (625 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc0u6mf_1/netbase_6.5_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libffi8 riscv64 3.5.2-4 [21.1 kB] Fetched 21.1 kB in 0s (1041 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc_9qti1z/libffi8_3.5.2-4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libsasl2-2 riscv64 2.1.28+dfsg1-11 [57.9 kB] Fetched 57.9 kB in 0s (2792 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyfvoe7fw/libsasl2-2_2.1.28+dfsg1-11_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libctf-nobfd0 riscv64 2.46-3 [163 kB] Fetched 163 kB in 0s (6578 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp_pzq7dr/libctf-nobfd0_2.46-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libnl-route-3-dev riscv64 3.12.0-2+b1 [626 kB] Fetched 626 kB in 0s (15.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl0cfj6bt/libnl-route-3-dev_3.12.0-2+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libselinux1 riscv64 3.10-1 [88.3 kB] Fetched 88.3 kB in 0s (4064 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd0c9lwz9/libselinux1_3.10-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-pybind11 all 3.0.1-3 [251 kB] Fetched 251 kB in 0s (5926 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8bvw9djb/python3-pybind11_3.0.1-3_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-mpi4py riscv64 4.1.1-9 [1121 kB] Fetched 1121 kB in 0s (25.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf3owo3yy/python3-mpi4py_4.1.1-9_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libgfortran-15-dev riscv64 15.2.0-17 [1308 kB] Fetched 1308 kB in 0s (27.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8ghncr1h/libgfortran-15-dev_15.2.0-17_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libnettle8t64 riscv64 3.10.2-1+b1 [331 kB] Fetched 331 kB in 0s (12.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxnf__gfj/libnettle8t64_3.10.2-1+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 python3-pytest all 9.0.3-1 [273 kB] Fetched 273 kB in 0s (10.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkr9k2d_a/python3-pytest_9.0.3-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 systemd riscv64 260.1-1 [3230 kB] Fetched 3230 kB in 0s (37.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbts8btz8/systemd_260.1-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libjansson4 riscv64 2.14-2+b4 [40.1 kB] Fetched 40.1 kB in 0s (1955 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe4v2xcx5/libjansson4_2.14-2+b4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 binutils riscv64 2.46-3 [285 kB] Fetched 285 kB in 0s (10.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm9m7mpb2/binutils_2.46-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libngtcp2-16 riscv64 1.22.1-1 [138 kB] Fetched 138 kB in 0s (6033 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5n9zphml/libngtcp2-16_1.22.1-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Fetched 250 kB in 0s (4318 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6ikc0b77/libjs-jquery-ui_1.13.2+dfsg-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libssh2-1t64 riscv64 1.11.1-3 [248 kB] Fetched 248 kB in 0s (9883 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprfwyxlgu/libssh2-1t64_1.11.1-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libdpkg-perl all 1.23.7 [669 kB] Fetched 669 kB 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dependency 215 of 281: bzip2:riscv64=1.0.8-6+b2 Downloading dependency 216 of 281: libpsl5t64:riscv64=0.21.5-1 Downloading dependency 217 of 281: libstdc++-15-dev:riscv64=15.2.0-17 Downloading dependency 218 of 281: librdmacm1t64:riscv64=63.0-1 Downloading dependency 219 of 281: openmpi-bin:riscv64=5.0.10-1 Downloading dependency 220 of 281: liblz4-1:riscv64=1.10.0-10 Downloading dependency 221 of 281: libfabric1:riscv64=2.1.0-1.1+b2 Downloading dependency 222 of 281: libtool:riscv64=2.5.4-11 Downloading dependency 223 of 281: libopenmpi-dev:riscv64=5.0.10-1 Downloading dependency 224 of 281: procps:riscv64=2:4.0.4-9+b2 Downloading dependency 225 of 281: libx11-data:riscv64=2:1.8.13-1 Downloading dependency 226 of 281: gzip:riscv64=1.13-1 Downloading dependency 227 of 281: libibmad5:riscv64=63.0-1 Downloading dependency 228 of 281: libcap-ng0:riscv64=0.9.3-1 Downloading dependency 229 of 281: libmpc3:riscv64=1.3.1-3 Downloading dependency 230 of 281: pybind11-dev:riscv64=3.0.1-3 Downloading dependency 231 of 281: hostname:riscv64=3.25 Downloading dependency 232 of 281: ocl-icd-libopencl1:riscv64=2.3.4-1+b1 Downloading dependency 233 of 281: netbase:riscv64=6.5 Downloading dependency 234 of 281: libffi8:riscv64=3.5.2-4 Downloading dependency 235 of 281: libsasl2-2:riscv64=2.1.28+dfsg1-11 Downloading dependency 236 of 281: libctf-nobfd0:riscv64=2.46-3 Downloading dependency 237 of 281: libnl-route-3-dev:riscv64=3.12.0-2+b1 Downloading dependency 238 of 281: libselinux1:riscv64=3.10-1 Downloading dependency 239 of 281: python3-pybind11:riscv64=3.0.1-3 Downloading dependency 240 of 281: python3-mpi4py:riscv64=4.1.1-9 Downloading dependency 241 of 281: libgfortran-15-dev:riscv64=15.2.0-17 Downloading dependency 242 of 281: libnettle8t64:riscv64=3.10.2-1+b1 Downloading dependency 243 of 281: python3-pytest:riscv64=9.0.3-1 Downloading dependency 244 of 281: systemd:riscv64=260.1-1 Downloading dependency 245 of 281: libjansson4:riscv64=2.14-2+b4 Downloading dependency 246 of 281: binutils:riscv64=2.46-3 Downloading dependency 247 of 281: libngtcp2-16:riscv64=1.22.1-1 Downloading dependency 248 of 281: libjs-jquery-ui:riscv64=1.13.2+dfsg-1 Downloading dependency 249 of 281: libssh2-1t64:riscv64=1.11.1-3 Downloading dependency 250 of 281: libdpkg-perl:riscv64=1.23.7 Downloading dependency 251 of 281: libfftw3-bin:riscv64=3.3.10-2+b2Get:1 http://deb.debian.org/debian unstable/main riscv64 libfftw3-bin riscv64 3.3.10-2+b2 [44.7 kB] Fetched 44.7 kB in 0s (827 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsz90zz4m/libfftw3-bin_3.3.10-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libibverbs1 riscv64 63.0-1 [62.5 kB] Fetched 62.5 kB in 0s (1135 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcpc2qk5a/libibverbs1_63.0-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libhwloc-dev riscv64 2.13.0-2 [575 kB] Fetched 575 kB in 0s (8415 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3nxh0nc4/libhwloc-dev_2.13.0-2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpython3.13-stdlib riscv64 3.13.12-1 [1936 kB] Fetched 1936 kB in 0s (31.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz2abal2e/libpython3.13-stdlib_3.13.12-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libk5crypto3 riscv64 1.22.1-2.1 [96.1 kB] Fetched 96.1 kB in 0s (4410 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpun25dwqr/libk5crypto3_1.22.1-2.1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 readline-common all 8.3-4 [74.8 kB] Fetched 74.8 kB in 0s (3511 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnayofdxg/readline-common_8.3-4_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 pkgconf riscv64 2.5.1-4 [33.6 kB] Fetched 33.6 kB in 0s (1624 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpig75k8_l/pkgconf_2.5.1-4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libpmix2t64 riscv64 6.0.0+really5.0.9-3+b1 [659 kB] Fetched 659 kB in 0s (9907 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphfgxvp6f/libpmix2t64_6.0.0+really5.0.9-3+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libsmartcols1 riscv64 2.42-6 [154 kB] Fetched 154 kB in 0s (6695 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeamyw54t/libsmartcols1_2.42-6_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libproc2-0 riscv64 2:4.0.4-9+b2 [62.8 kB] Fetched 62.8 kB in 0s (3002 kB/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-9+b2_riscv64.deb' to '/srv/rebuilderd/tmp/tmpmyel3wu9/libproc2-0_4.0.4-9+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libctf0 riscv64 2.46-3 [96.1 kB] Fetched 96.1 kB in 0s (4285 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp963c4mka/libctf0_2.46-3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libxnvctrl0 riscv64 535.171.04-1+b3 [14.6 kB] Fetched 14.6 kB in 0s (279 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp959ddsfq/libxnvctrl0_535.171.04-1+b3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libfftw3-dev riscv64 3.3.10-2+b2 [1479 kB] Fetched 1479 kB in 0s (28.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnvi0scrs/libfftw3-dev_3.3.10-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 debhelper all 13.31 [932 kB] Fetched 932 kB in 0s (23.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmv0msms4/debhelper_13.31_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20260514T022936Z forky/main riscv64 libdebconfclient0 riscv64 0.282+b3 [7576 B] Fetched 7576 B in 0s (381 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1ie1nadu/libdebconfclient0_0.282+b3_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 init-system-helpers all 1.69 [39.3 kB] Fetched 39.3 kB in 0s (1939 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsvi0xqmd/init-system-helpers_1.69_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libxext6 riscv64 2:1.3.4-1+b4 [51.1 kB] Fetched 51.1 kB in 0s (2456 kB/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b4_riscv64.deb' to '/srv/rebuilderd/tmp/tmpmgh7l1y4/libxext6_1.3.4-1+b4_riscv64.deb' Get:1 http://snapshot.debian.org/archive/debian/20260514T022936Z forky/main riscv64 libmd0 riscv64 1.1.0-2+b2 [36.7 kB] Fetched 36.7 kB in 0s (1808 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_oprnns8/libmd0_1.1.0-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 gcc riscv64 4:15.2.0-5+b1 [5156 B] Fetched 5156 B in 0s (96.9 kB/s) dpkg-name: info: moved 'gcc_4%3a15.2.0-5+b1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpq_put3tv/gcc_15.2.0-5+b1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 diffutils riscv64 1:3.12-1 [405 kB] Fetched 405 kB in 0s (14.2 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.12-1_riscv64.deb' to '/srv/rebuilderd/tmp/tmpvsawqfg9/diffutils_3.12-1_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libfftw3-long3 riscv64 3.3.10-2+b2 [701 kB] Fetched 701 kB in 0s (10.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkmm9vt9v/libfftw3-long3_3.3.10-2+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libaudit-common all 1:4.1.2-1 [14.3 kB] Fetched 14.3 kB in 0s (722 kB/s) dpkg-name: info: moved 'libaudit-common_1%3a4.1.2-1_all.deb' to '/srv/rebuilderd/tmp/tmpnz__xtqf/libaudit-common_4.1.2-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libattr1 riscv64 1:2.5.2-4 [23.0 kB] Fetched 23.0 kB in 0s (1143 kB/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-4_riscv64.deb' to '/srv/rebuilderd/tmp/tmpeymb7jpo/libattr1_2.5.2-4_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (1136 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn3enpjdy/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (1841 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_jm7lifd/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libc-dev-bin riscv64 2.42-16 [36.7 kB] Fetched 36.7 kB in 0s (1795 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4_4jg3io/libc-dev-bin_2.42-16_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libltdl-dev riscv64 2.5.4-11 [193 kB] Fetched 193 kB in 0s (3395 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv7ekcpes/libltdl-dev_2.5.4-11_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libmagic1t64 riscv64 1:5.46-5+b2 [116 kB] Fetched 116 kB in 0s (5216 kB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-5+b2_riscv64.deb' to '/srv/rebuilderd/tmp/tmp7u2p_ky7/libmagic1t64_5.46-5+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libbz2-1.0 riscv64 1.0.8-6+b2 [39.6 kB] Fetched 39.6 kB in 0s (1947 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps74giugc/libbz2-1.0_1.0.8-6+b2_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libc-gconv-modules-extra riscv64 2.42-16 [1105 kB] Fetched 1105 kB in 0s (25.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl0bkdun0/libc-gconv-modules-extra_2.42-16_riscv64.deb' Get:1 http://deb.debian.org/debian unstable/main riscv64 libncursesw6 riscv64 6.6+20251231-1+b1 [141 kB] Fetched 141 kB in 0s (6174 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprpyxy5y1/libncursesw6_6.6+20251231-1+b1_riscv64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_riscv64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_riscv64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmpq4iym_98/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture riscv64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.fB_1MzsrCi as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.fB_1MzsrCi 127.0.0.1 - - [15/May/2026 07:12:07] code 404, message File not found 127.0.0.1 - - [15/May/2026 07:12:07] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:44215 ./ InRelease 127.0.0.1 - - [15/May/2026 07:12:07] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:44215 ./ Release [462 B] 127.0.0.1 - - [15/May/2026 07:12:07] code 404, message File not found 127.0.0.1 - - [15/May/2026 07:12:07] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:44215 ./ Release.gpg 127.0.0.1 - - [15/May/2026 07:12:07] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:44215 ./ Packages [346 kB] Fetched 347 kB in 0s (6920 kB/s) Reading package lists... usr-is-merged found but not real -- not running merged-usr setup hook I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [15/May/2026 07:12:07] "GET /./gcc-16-base_16-20260425-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:07] "GET /./libc-gconv-modules-extra_2.42-16_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:07] "GET /./libc6_2.42-16_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./libgcc-s1_16-20260425-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./mawk_1.3.4.20260302-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./base-files_14_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./libtinfo6_6.6%2b20251231-1%2bb1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./debianutils_5.23.2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./bash_5.3-3_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./libacl1_2.3.2-3_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./libattr1_2.5.2-4_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./libgmp10_6.3.0%2bdfsg-5%2bb1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./libpcre2-8-0_10.46-1%2bb2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./libselinux1_3.10-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./libzstd1_1.5.7%2bdfsg-3%2bb2_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./zlib1g_1.3.dfsg%2breally1.3.2-3_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./libssl3t64_3.6.2-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./openssl-provider-legacy_3.6.2-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./libsystemd0_260.1-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./coreutils_9.10-1_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./dash_0.5.12-12_riscv64.deb HTTP/1.1" 200 - 127.0.0.1 - - [15/May/2026 07:12:08] "GET /./diffutils_3.12-1_riscv64.deb HTTP/1.1" 200 - 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127.0.0.1 - - [15/May/2026 07:12:08] "GET /./sysvinit-utils_3.18-1_riscv64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.fB_1MzsrCi 127.0.0.1 - - [15/May/2026 07:12:12] code 404, message File not found 127.0.0.1 - - [15/May/2026 07:12:12] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:44215 ./ InRelease 127.0.0.1 - - [15/May/2026 07:12:12] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:44215 ./ Release 127.0.0.1 - - [15/May/2026 07:12:12] code 404, message File not found 127.0.0.1 - - [15/May/2026 07:12:12] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:44215 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... 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I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpq4iym_98/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.fB_1MzsrCi Reading package lists... Building dependency tree... Reading state information... libjs-sphinxdoc is already the newest version (9.1.0-3). libjs-sphinxdoc set to manually installed. libc6 is already the newest version (2.42-16). python3 is already the newest version (3.13.9-3+b1). python3 set to manually installed. cpp-riscv64-linux-gnu is already the newest version (4:15.2.0-5+b1). cpp-riscv64-linux-gnu set to manually installed. libedit2 is already the newest version (3.1-20251016-1+b1). libedit2 set to manually installed. libhwloc15 is already the newest version (2.13.0-2). libhwloc15 set to manually installed. libpipeline1 is already the newest version (1.5.8-3). libpipeline1 set to manually installed. libelf1t64 is already the newest version (0.195-1). libelf1t64 set to manually installed. tzdata is already the newest version (2026b-1). tzdata set to manually installed. libsframe3 is already the newest version (2.46-3). libsframe3 set to manually installed. libfftw3-single3 is already the newest version (3.3.10-2+b2). libfftw3-single3 set to manually installed. bsdextrautils is already the newest version (2.42-6). bsdextrautils set to manually installed. autotools-dev is already the newest version (20240727.1+nmu1). autotools-dev set to manually installed. libgdbm6t64 is already the newest version (1.26-1+b2). libgdbm6t64 set to manually installed. libbinutils is already the newest version (2.46-3). libbinutils set to manually installed. libdebhelper-perl is already the newest version (13.31). libdebhelper-perl set to manually installed. libmount1 is already the newest version (2.42-6). libnuma-dev is already the newest version (2.0.19-1+b2). libnuma-dev set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1+b2). rpcsvc-proto set to manually installed. liblzma5 is already the newest version (5.8.3-1). g++ is already the newest version (4:15.2.0-5+b1). g++ set to manually installed. linux-libc-dev is already the newest version (7.0.4-1). linux-libc-dev set to manually installed. libpython3-stdlib is already the newest version (3.13.9-3+b1). libpython3-stdlib set to manually installed. libgdbm-compat4t64 is already the newest version (1.26-1+b2). libgdbm-compat4t64 set to manually installed. liblapack-dev is already the newest version (3.12.1-7+b1). liblapack-dev set to manually installed. libnghttp2-14 is already the newest version (1.69.0-1). libnghttp2-14 set to manually installed. mount is already the newest version (2.42-6). mount set to manually installed. libuchardet0 is already the newest version (0.0.8-2+b2). libuchardet0 set to manually installed. libtinfo6 is already the newest version (6.6+20251231-1+b1). libpython3-dev is already the newest version (3.13.9-3+b1). libpython3-dev set to manually installed. libaudit1 is already the newest version (1:4.1.2-1+b1). libboost1.90-dev is already the newest version (1.90.0-6). libboost1.90-dev set to manually installed. libkrb5support0 is already the newest version (1.22.1-2.1). libkrb5support0 set to manually installed. gettext is already the newest version (0.23.2-2). gettext set to manually installed. libblas3 is already the newest version (3.12.1-7+b1). libblas3 set to manually installed. libxau6 is already the newest version (1:1.0.11-1+b2). libxau6 set to manually installed. libjsoncpp26 is already the newest version (1.9.7-2). libjsoncpp26 set to manually installed. lsb-release is already the newest version (12.1-2). lsb-release set to manually installed. libcrypt1 is already the newest version (1:4.5.1-1+b1). sed is already the newest version (4.9-3). gfortran-15-riscv64-linux-gnu is already the newest version (15.2.0-17). gfortran-15-riscv64-linux-gnu set to manually installed. libevent-pthreads-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-pthreads-2.1-7t64 set to manually installed. binutils-riscv64-linux-gnu is already the newest version (2.46-3). binutils-riscv64-linux-gnu set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-5+b1). python3-numpy is already the newest version (1:2.4.4+ds-2). python3-numpy set to manually installed. g++-riscv64-linux-gnu is already the newest version (4:15.2.0-5+b1). g++-riscv64-linux-gnu set to manually installed. libsqlite3-0 is already the newest version (3.46.1-9+b1). libsqlite3-0 set to manually installed. libuuid1 is already the newest version (2.42-6). perl-base is already the newest version (5.40.1-7+b1). autopoint is already the newest version (0.23.2-2). autopoint set to manually installed. libblkid1 is already the newest version (2.42-6). python3-pluggy is already the newest version (1.6.0-2). python3-pluggy set to manually installed. automake is already the newest version (1:1.18.1-4). automake set to manually installed. libpcre2-8-0 is already the newest version (10.46-1+b2). ncurses-base is already the newest version (6.6+20251231-1). python3.13 is already the newest version (3.13.12-1). python3.13 set to manually installed. gcc-15 is already the newest version (15.2.0-17). gcc-15 set to manually installed. bash is already the newest version (5.3-3). python3-networkx is already the newest version (3.4.2-5). python3-networkx set to manually installed. libmuparser-dev is already the newest version (2.3.4-2+b1). libmuparser-dev set to manually installed. libbsd0 is already the newest version (0.12.2-2+b2). libbsd0 set to manually installed. libnl-3-dev is already the newest version (3.12.0-2+b1). libnl-3-dev set to manually installed. libreadline8t64 is already the newest version (8.3-4). libreadline8t64 set to manually installed. libxdmcp6 is already the newest version (1:1.1.5-2+b1). libxdmcp6 set to manually installed. cmake is already the newest version (4.3.2-1). cmake set to manually installed. gfortran-15 is already the newest version (15.2.0-17). gfortran-15 set to manually installed. libcc1-0 is already the newest version (16-20260425-1). libcc1-0 set to manually installed. bash-completion is already the newest version (1:2.16.0-8). bash-completion set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-7). perl-modules-5.40 set to manually installed. findutils is already the newest version (4.10.0-4). python3-iniconfig is already the newest version (2.1.0-2). python3-iniconfig set to manually installed. python3-pygments is already the newest version (2.19.2+dfsg-1). python3-pygments set to manually installed. libbrotli1 is already the newest version (1.2.0-3). libbrotli1 set to manually installed. libprrte-bin is already the newest version (3.0.13-3). libprrte-bin set to manually installed. libexpat1 is already the newest version (2.8.0-2). libexpat1 set to manually installed. libprrte3 is already the newest version (3.0.13-3). libprrte3 set to manually installed. libxml2-16 is already the newest version (2.15.2+dfsg-0.1). libxml2-16 set to manually installed. cpp is already the newest version (4:15.2.0-5+b1). cpp set to manually installed. m4 is already the newest version (1.4.21-1). m4 set to manually installed. python3.13-dev is already the newest version (3.13.12-1). python3.13-dev set to manually installed. libfuse3-4 is already the newest version (3.18.2-2). libfuse3-4 set to manually installed. libpam0g is already the newest version (1.7.0-5+b1). libuv1t64 is already the newest version (1.51.0-2+b2). libuv1t64 set to manually installed. libfido2-1 is already the newest version (1.17.0-1). libfido2-1 set to manually installed. libisl23 is already the newest version (0.27-2). libisl23 set to manually installed. coreutils is already the newest version (9.10-1). libnl-route-3-200 is already the newest version (3.12.0-2+b1). libnl-route-3-200 set to manually installed. libldap2 is already the newest version (2.6.10+dfsg-1+b1). libldap2 set to manually installed. g++-15-riscv64-linux-gnu is already the newest version (15.2.0-17). g++-15-riscv64-linux-gnu set to manually installed. dash is already the newest version (0.5.12-12). mpi-default-bin is already the newest version (1.20). mpi-default-bin set to manually installed. libjs-jquery is already the newest version (3.7.1+dfsg+~3.5.33-1). libjs-jquery set to manually installed. libnghttp3-9 is already the newest version (1.15.0-1). libnghttp3-9 set to manually installed. pkgconf-bin is already the newest version (2.5.1-4). pkgconf-bin set to manually installed. libucx0 is already the newest version (1.20.1~rc2-1). libucx0 set to manually installed. libtsan2 is already the newest version (16-20260425-1). libtsan2 set to manually installed. python3-minimal is already the newest version (3.13.9-3+b1). python3-minimal set to manually installed. libubsan1 is already the newest version (16-20260425-1). libubsan1 set to manually installed. python3.13-minimal is already the newest version (3.13.12-1). python3.13-minimal set to manually installed. base-passwd is already the newest version (3.6.8). dwz is already the newest version (0.16-4). dwz set to manually installed. debconf is already the newest version (1.5.92). libboost-dev is already the newest version (1.90.0.2). libboost-dev set to manually installed. libgfortran5 is already the newest version (16-20260425-1). libgfortran5 set to manually installed. libmunge2 is already the newest version (0.5.18-1). libmunge2 set to manually installed. libevent-core-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-core-2.1-7t64 set to manually installed. libgprofng0 is already the newest version (2.46-3). libgprofng0 set to manually installed. libpciaccess0 is already the newest version (0.17-3+b4). libpciaccess0 set to manually installed. libx11-6 is already the newest version (2:1.8.13-1). libx11-6 set to manually installed. openssl-provider-legacy is already the newest version (3.6.2-1). man-db is already the newest version (2.13.1-1). man-db set to manually installed. python3-dev is already the newest version (3.13.9-3+b1). python3-dev set to manually installed. libidn2-0 is already the newest version (2.3.8-5). libidn2-0 set to manually installed. librhash1 is already the newest version (1.4.6-1.1+b1). librhash1 set to manually installed. libxcb1 is already the newest version (1.17.0-2+b2). libxcb1 set to manually installed. libxxhash0 is already the newest version (0.8.3-2+b2). libxxhash0 set to manually installed. xz-utils is already the newest version (5.8.3-1). xz-utils set to manually installed. libacl1 is already the newest version (2.3.2-3). libhwloc-plugins is already the newest version (2.13.0-2). libhwloc-plugins set to manually installed. gcc-15-riscv64-linux-gnu is already the newest version (15.2.0-17). gcc-15-riscv64-linux-gnu set to manually installed. libudev1 is already the newest version (260.1-1). libstdc++6 is already the newest version (16-20260425-1). libstdc++6 set to manually installed. mawk is already the newest version (1.3.4.20260302-1). dh-autoreconf is already the newest version (22). dh-autoreconf set to manually installed. po-debconf is already the newest version (1.0.22). po-debconf set to manually installed. libperl5.40 is already the newest version (5.40.1-7+b1). libperl5.40 set to manually installed. autoconf is already the newest version (2.72-6). autoconf set to manually installed. base-files is already the newest version (14). libgcc-15-dev is already the newest version (15.2.0-17). libgcc-15-dev set to manually installed. libgcc-s1 is already the newest version (16-20260425-1). libngtcp2-crypto-ossl0 is already the newest version (1.22.1-1). libngtcp2-crypto-ossl0 set to manually installed. ibverbs-providers is already the newest version (63.0-1). ibverbs-providers set to manually installed. libevent-dev is already the newest version (2.1.12-stable-10+b2). libevent-dev set to manually installed. python3-numpy-dev is already the newest version (1:2.4.4+ds-2). python3-numpy-dev set to manually installed. dh-python is already the newest version (7.20260309). dh-python set to manually installed. libpam-modules is already the newest version (1.7.0-5+b1). libfftw3-double3 is already the newest version (3.3.10-2+b2). libfftw3-double3 set to manually installed. libltdl7 is already the newest version (2.5.4-11). libltdl7 set to manually installed. libmagic-mgc is already the newest version (1:5.46-5+b2). libmagic-mgc set to manually installed. libmuparser2v5 is already the newest version (2.3.4-2+b1). libmuparser2v5 set to manually installed. patch is already the newest version (2.8-2). patch set to manually installed. grep is already the newest version (3.12-1). libgssapi-krb5-2 is already the newest version (1.22.1-2.1). libgssapi-krb5-2 set to manually installed. libitm1 is already the newest version (16-20260425-1). libitm1 set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.2-3). zlib1g-dev set to manually installed. libpam-runtime is already the newest version (1.7.0-5). libcurl4t64 is already the newest version (8.20.0-1). libcurl4t64 set to manually installed. libatomic1 is already the newest version (16-20260425-1). libatomic1 set to manually installed. libkrb5-3 is already the newest version (1.22.1-2.1). libkrb5-3 set to manually installed. libssl3t64 is already the newest version (3.6.2-1). file is already the newest version (1:5.46-5+b2). file set to manually installed. libcbor0.10 is already the newest version (0.10.2-2.1+b1). libcbor0.10 set to manually installed. libunistring5 is already the newest version (1.4.2-1). libunistring5 set to manually installed. gcc-riscv64-linux-gnu is already the newest version (4:15.2.0-5+b1). gcc-riscv64-linux-gnu set to manually installed. libsystemd-shared is already the newest version (260.1-1). libsystemd-shared set to manually installed. groff-base is already the newest version (1.24.1-1). groff-base set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.2-3). libnl-3-200 is already the newest version (3.12.0-2+b1). libnl-3-200 set to manually installed. gettext-base is already the newest version (0.23.2-2). gettext-base set to manually installed. liblsan0 is already the newest version (16-20260425-1). liblsan0 set to manually installed. libibverbs-dev is already the newest version (63.0-1). libibverbs-dev set to manually installed. libpython3.13-minimal is already the newest version (3.13.12-1). libpython3.13-minimal set to manually installed. gcc-15-base is already the newest version (15.2.0-17). gcc-15-base set to manually installed. ncurses-bin is already the newest version (6.6+20251231-1+b1). sysvinit-utils is already the newest version (3.18-1). binutils-common is already the newest version (2.46-3). binutils-common set to manually installed. libopenmpi40 is already the newest version (5.0.10-1). libopenmpi40 set to manually installed. libkeyutils1 is already the newest version (1.6.3-6+b2). libkeyutils1 set to manually installed. gcc-16-base is already the newest version (16-20260425-1). libsystemd0 is already the newest version (260.1-1). dh-strip-nondeterminism is already the newest version (1.15.0-1). dh-strip-nondeterminism set to manually installed. libevent-extra-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-extra-2.1-7t64 set to manually installed. mpi-default-dev is already the newest version (1.20). mpi-default-dev set to manually installed. openmpi-common is already the newest version (5.0.10-1). openmpi-common set to manually installed. architecture-properties is already the newest version (0.2.6+b2). architecture-properties set to manually installed. dpkg is already the newest version (1.23.7). perl is already the newest version (5.40.1-7+b1). perl set to manually installed. libpkgconf7 is already the newest version (2.5.1-4). libpkgconf7 set to manually installed. libasan8 is already the newest version (16-20260425-1). libasan8 set to manually installed. libevent-openssl-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-openssl-2.1-7t64 set to manually installed. util-linux is already the newest version (2.42-6). liblapack3 is already the newest version (3.12.1-7+b1). liblapack3 set to manually installed. libmpfr6 is already the newest version (4.2.2-3). libmpfr6 set to manually installed. libpython3.13 is already the newest version (3.13.12-1). libpython3.13 set to manually installed. libucc1 is already the newest version (1.7.0~rc1-1). libucc1 set to manually installed. libexpat1-dev is already the newest version (2.8.0-2). libexpat1-dev set to manually installed. libzstd1 is already the newest version (1.5.7+dfsg-3+b2). dpkg-dev is already the newest version (1.23.7). dpkg-dev set to manually installed. sensible-utils is already the newest version (0.0.26). sensible-utils set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-11). libsasl2-modules-db set to manually installed. libc6-dev is already the newest version (2.42-16). libc6-dev set to manually installed. cpp-15 is already the newest version (15.2.0-17). cpp-15 set to manually installed. tar is already the newest version (1.35+dfsg-4). build-essential is already the newest version (12.12). build-essential set to manually installed. libblas-dev is already the newest version (3.12.1-7+b1). libblas-dev set to manually installed. libarchive13t64 is already the newest version (3.8.7-1). libarchive13t64 set to manually installed. libcom-err2 is already the newest version (1.47.4-1). libcom-err2 set to manually installed. libpam-modules-bin is already the newest version (1.7.0-5+b1). libdb5.3t64 is already the newest version (5.3.28+dfsg2-11+b1). libgomp1 is already the newest version (16-20260425-1). libgomp1 set to manually installed. libprrte-dev is already the newest version (3.0.13-3). libprrte-dev set to manually installed. python3-packaging is already the newest version (26.0-1). python3-packaging set to manually installed. libpython3.13-dev is already the newest version (3.13.12-1). libpython3.13-dev set to manually installed. make is already the newest version (4.4.1-3). make set to manually installed. g++-15 is already the newest version (15.2.0-17). g++-15 set to manually installed. media-types is already the newest version (14.0.0). media-types set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.15.0-1). libfile-stripnondeterminism-perl set to manually installed. libc-bin is already the newest version (2.42-16). openssh-client is already the newest version (1:10.3p1-2). openssh-client set to manually installed. debianutils is already the newest version (5.23.2). libnuma1 is already the newest version (2.0.19-1+b2). libnuma1 set to manually installed. cpp-15-riscv64-linux-gnu is already the newest version (15.2.0-17). cpp-15-riscv64-linux-gnu set to manually installed. libevent-2.1-7t64 is already the newest version (2.1.12-stable-10+b2). libevent-2.1-7t64 set to manually installed. libibumad3 is already the newest version (63.0-1). libibumad3 set to manually installed. bzip2 is already the newest version (1.0.8-6+b2). bzip2 set to manually installed. libpsl5t64 is already the newest version (0.21.5-1). libpsl5t64 set to manually installed. libstdc++-15-dev is already the newest version (15.2.0-17). libstdc++-15-dev set to manually installed. librdmacm1t64 is already the newest version (63.0-1). librdmacm1t64 set to manually installed. openmpi-bin is already the newest version (5.0.10-1). openmpi-bin set to manually installed. liblz4-1 is already the newest version (1.10.0-10). liblz4-1 set to manually installed. libfabric1 is already the newest version (2.1.0-1.1+b2). libfabric1 set to manually installed. libtool is already the newest version (2.5.4-11). libtool set to manually installed. libopenmpi-dev is already the newest version (5.0.10-1). libopenmpi-dev set to manually installed. procps is already the newest version (2:4.0.4-9+b2). procps set to manually installed. libx11-data is already the newest version (2:1.8.13-1). libx11-data set to manually installed. gzip is already the newest version (1.13-1). libibmad5 is already the newest version (63.0-1). libibmad5 set to manually installed. libcap-ng0 is already the newest version (0.9.3-1). libmpc3 is already the newest version (1.3.1-3). libmpc3 set to manually installed. pybind11-dev is already the newest version (3.0.1-3). pybind11-dev set to manually installed. hostname is already the newest version (3.25). ocl-icd-libopencl1 is already the newest version (2.3.4-1+b1). ocl-icd-libopencl1 set to manually installed. netbase is already the newest version (6.5). netbase set to manually installed. libffi8 is already the newest version (3.5.2-4). libffi8 set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-11). libsasl2-2 set to manually installed. libctf-nobfd0 is already the newest version (2.46-3). libctf-nobfd0 set to manually installed. libnl-route-3-dev is already the newest version (3.12.0-2+b1). libnl-route-3-dev set to manually installed. libselinux1 is already the newest version (3.10-1). python3-pybind11 is already the newest version (3.0.1-3). python3-pybind11 set to manually installed. python3-mpi4py is already the newest version (4.1.1-9). python3-mpi4py set to manually installed. libgfortran-15-dev is already the newest version (15.2.0-17). libgfortran-15-dev set to manually installed. libnettle8t64 is already the newest version (3.10.2-1+b1). libnettle8t64 set to manually installed. python3-pytest is already the newest version (9.0.3-1). python3-pytest set to manually installed. systemd is already the newest version (260.1-1). systemd set to manually installed. libjansson4 is already the newest version (2.14-2+b4). libjansson4 set to manually installed. binutils is already the newest version (2.46-3). binutils set to manually installed. libngtcp2-16 is already the newest version (1.22.1-1). libngtcp2-16 set to manually installed. libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. libssh2-1t64 is already the newest version (1.11.1-3). libssh2-1t64 set to manually installed. libdpkg-perl is already the newest version (1.23.7). libdpkg-perl set to manually installed. libfftw3-bin is already the newest version (3.3.10-2+b2). libfftw3-bin set to manually installed. libibverbs1 is already the newest version (63.0-1). libibverbs1 set to manually installed. libhwloc-dev is already the newest version (2.13.0-2). libhwloc-dev set to manually installed. libpython3.13-stdlib is already the newest version (3.13.12-1). libpython3.13-stdlib set to manually installed. libk5crypto3 is already the newest version (1.22.1-2.1). libk5crypto3 set to manually installed. readline-common is already the newest version (8.3-4). readline-common set to manually installed. pkgconf is already the newest version (2.5.1-4). pkgconf set to manually installed. libpmix2t64 is already the newest version (6.0.0+really5.0.9-3+b1). libpmix2t64 set to manually installed. libsmartcols1 is already the newest version (2.42-6). libproc2-0 is already the newest version (2:4.0.4-9+b2). libproc2-0 set to manually installed. libctf0 is already the newest version (2.46-3). libctf0 set to manually installed. libxnvctrl0 is already the newest version (535.171.04-1+b3). libxnvctrl0 set to manually installed. libfftw3-dev is already the newest version (3.3.10-2+b2). libfftw3-dev set to manually installed. debhelper is already the newest version (13.31). debhelper set to manually installed. libdebconfclient0 is already the newest version (0.282+b3). init-system-helpers is already the newest version (1.69). libxext6 is already the newest version (2:1.3.4-1+b4). libxext6 set to manually installed. libmd0 is already the newest version (1.1.0-2+b2). gcc is already the newest version (4:15.2.0-5+b1). gcc set to manually installed. diffutils is already the newest version (1:3.12-1). libfftw3-long3 is already the newest version (3.3.10-2+b2). libfftw3-long3 set to manually installed. libaudit-common is already the newest version (1:4.1.2-1). libattr1 is already the newest version (1:2.5.2-4). intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libc-dev-bin is already the newest version (2.42-16). libc-dev-bin set to manually installed. libltdl-dev is already the newest version (2.5.4-11). libltdl-dev set to manually installed. libmagic1t64 is already the newest version (1:5.46-5+b2). libmagic1t64 set to manually installed. libbz2-1.0 is already the newest version (1.0.8-6+b2). libc-gconv-modules-extra is already the newest version (2.42-16). libncursesw6 is already the newest version (6.6+20251231-1+b1). libncursesw6 set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.fB_1MzsrCi (Reading database ... 47772 files and directories currently installed.) Removing debootsnap-dummy (1.0) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg-query --showformat '${binary:Package}=${Version}\n' --show > "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.fB_1MzsrCi I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.fB_1MzsrCi I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: cleaning package lists and apt cache... I: skipping cleanup/reproducible as requested I: creating tarball... I: done I: removing tempdir /srv/rebuilderd/tmp/mmdebstrap.fB_1MzsrCi... I: success in 325.9804 seconds Downloading dependency 252 of 281: libibverbs1:riscv64=63.0-1 Downloading dependency 253 of 281: libhwloc-dev:riscv64=2.13.0-2 Downloading dependency 254 of 281: libpython3.13-stdlib:riscv64=3.13.12-1 Downloading dependency 255 of 281: libk5crypto3:riscv64=1.22.1-2.1 Downloading dependency 256 of 281: readline-common:riscv64=8.3-4 Downloading dependency 257 of 281: pkgconf:riscv64=2.5.1-4 Downloading dependency 258 of 281: libpmix2t64:riscv64=6.0.0+really5.0.9-3+b1 Downloading dependency 259 of 281: libsmartcols1:riscv64=2.42-6 Downloading dependency 260 of 281: libproc2-0:riscv64=2:4.0.4-9+b2 Downloading dependency 261 of 281: libctf0:riscv64=2.46-3 Downloading dependency 262 of 281: libxnvctrl0:riscv64=535.171.04-1+b3 Downloading dependency 263 of 281: libfftw3-dev:riscv64=3.3.10-2+b2 Downloading dependency 264 of 281: debhelper:riscv64=13.31 Downloading dependency 265 of 281: libdebconfclient0:riscv64=0.282+b3 Downloading dependency 266 of 281: init-system-helpers:riscv64=1.69 Downloading dependency 267 of 281: libxext6:riscv64=2:1.3.4-1+b4 Downloading dependency 268 of 281: libmd0:riscv64=1.1.0-2+b2 Downloading dependency 269 of 281: gcc:riscv64=4:15.2.0-5+b1 Downloading dependency 270 of 281: diffutils:riscv64=1:3.12-1 Downloading dependency 271 of 281: libfftw3-long3:riscv64=3.3.10-2+b2 Downloading dependency 272 of 281: libaudit-common:riscv64=1:4.1.2-1 Downloading dependency 273 of 281: libattr1:riscv64=1:2.5.2-4 Downloading dependency 274 of 281: intltool-debian:riscv64=0.35.0+20060710.6 Downloading dependency 275 of 281: libarchive-zip-perl:riscv64=1.68-1 Downloading dependency 276 of 281: libc-dev-bin:riscv64=2.42-16 Downloading dependency 277 of 281: libltdl-dev:riscv64=2.5.4-11 Downloading dependency 278 of 281: libmagic1t64:riscv64=1:5.46-5+b2 Downloading dependency 279 of 281: libbz2-1.0:riscv64=1.0.8-6+b2 Downloading dependency 280 of 281: libc-gconv-modules-extra:riscv64=2.42-16 Downloading dependency 281 of 281: libncursesw6:riscv64=6.6+20251231-1+b1 env --chdir=/srv/rebuilderd/tmp/rebuilderdHqcnof/out DEB_BUILD_OPTIONS=parallel=4 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1778600100 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildGTYdLF/debrebuild.sbuildrc.zZapCwQmUMnv sbuild --build=riscv64 --host=riscv64 --arch-any --no-arch-all --chroot=/srv/rebuilderd/tmp/debrebuildGTYdLF/debrebuild.tar.pMEvNyFPFv1s --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --no-source --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=gromacs-2026.2 /srv/rebuilderd/tmp/rebuilderdHqcnof/inputs/gromacs_2026.2-2.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on localhost +==============================================================================+ | gromacs 2026.2-2 (riscv64) Thu, 14 May 2026 23:17:34 +0000 | +==============================================================================+ Package: gromacs Version: 2026.2-2 Source Version: 2026.2-2 Distribution: unstable Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildGTYdLF/debrebuild.tar.pMEvNyFPFv1s to /srv/rebuilderd/tmp/tmp.sbuild.VieHAMV0MX... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Thu, 14 May 2026 23:18:07 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdHqcnof/inputs/gromacs_2026.2-2.dsc exists in /srv/rebuilderd/tmp/rebuilderdHqcnof/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Thu, 14 May 2026 23:18:29 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: architecture-is-64-bit, bash-completion, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, make (>= 4.4), mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, build-essential Filtered Build-Depends: architecture-is-64-bit, bash-completion, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, make (>= 4.4), mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-Q4DW3c/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Thu, 14 May 2026 23:18:42 +0000 | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment Thu, 14 May 2026 23:18:43 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.6.87-win2030 #2025.04.20.18.43+bb0c69aea SMP Sun Apr 20 18:58:14 UTC 2025 riscv64 (riscv64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-15_15.2.0-17 gcc-15_15.2.0-17 libc6-dev_2.42-16 libstdc++-15-dev_15.2.0-17 libstdc++6_16-20260425-1 linux-libc-dev_7.0.4-1 Package versions: architecture-properties_0.2.6+b2 autoconf_2.72-6 automake_1:1.18.1-4 autopoint_0.23.2-2 autotools-dev_20240727.1+nmu1 base-files_14 base-passwd_3.6.8 bash_5.3-3 bash-completion_1:2.16.0-8 binutils_2.46-3 binutils-common_2.46-3 binutils-riscv64-linux-gnu_2.46-3 bsdextrautils_2.42-6 build-essential_12.12 bzip2_1.0.8-6+b2 cmake_4.3.2-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.2.0-17 cpp-15-riscv64-linux-gnu_15.2.0-17 cpp-riscv64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_13.31 debianutils_5.23.2 dh-autoreconf_22 dh-python_7.20260309 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 file_1:5.46-5+b2 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.2.0-17 g++-15-riscv64-linux-gnu_15.2.0-17 g++-riscv64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.2.0-17 gcc-15-base_15.2.0-17 gcc-15-riscv64-linux-gnu_15.2.0-17 gcc-16-base_16-20260425-1 gcc-riscv64-linux-gnu_4:15.2.0-5+b1 gettext_0.23.2-2 gettext-base_0.23.2-2 gfortran-15_15.2.0-17 gfortran-15-riscv64-linux-gnu_15.2.0-17 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 ibverbs-providers_63.0-1 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libarchive-zip-perl_1.68-1 libarchive13t64_3.8.7-1 libasan8_16-20260425-1 libatomic1_16-20260425-1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-3 libblas-dev_3.12.1-7+b1 libblas3_3.12.1-7+b1 libblkid1_2.42-6 libboost-dev_1.90.0.2 libboost1.90-dev_1.90.0-6 libbrotli1_1.2.0-3 libbsd0_0.12.2-2+b2 libbz2-1.0_1.0.8-6+b2 libc-bin_2.42-16 libc-dev-bin_2.42-16 libc-gconv-modules-extra_2.42-16 libc6_2.42-16 libc6-dev_2.42-16 libcap-ng0_0.9.3-1 libcbor0.10_0.10.2-2.1+b1 libcc1-0_16-20260425-1 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libcurl4t64_8.20.0-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.282+b3 libdebhelper-perl_13.31 libdpkg-perl_1.23.7 libedit2_3.1-20251016-1+b1 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.12-stable-10+b2 libevent-core-2.1-7t64_2.1.12-stable-10+b2 libevent-dev_2.1.12-stable-10+b2 libevent-extra-2.1-7t64_2.1.12-stable-10+b2 libevent-openssl-2.1-7t64_2.1.12-stable-10+b2 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b2 libexpat1_2.8.0-2 libexpat1-dev_2.8.0-2 libfabric1_2.1.0-1.1+b2 libffi8_3.5.2-4 libfftw3-bin_3.3.10-2+b2 libfftw3-dev_3.3.10-2+b2 libfftw3-double3_3.3.10-2+b2 libfftw3-long3_3.3.10-2+b2 libfftw3-single3_3.3.10-2+b2 libfido2-1_1.17.0-1 libfile-stripnondeterminism-perl_1.15.0-1 libfuse3-4_3.18.2-2 libgcc-15-dev_15.2.0-17 libgcc-s1_16-20260425-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgfortran-15-dev_15.2.0-17 libgfortran5_16-20260425-1 libgmp10_2:6.3.0+dfsg-5+b1 libgomp1_16-20260425-1 libgprofng0_2.46-3 libgssapi-krb5-2_1.22.1-2.1 libhwloc-dev_2.13.0-2 libhwloc-plugins_2.13.0-2 libhwloc15_2.13.0-2 libibmad5_63.0-1 libibumad3_63.0-1 libibverbs-dev_63.0-1 libibverbs1_63.0-1 libidn2-0_2.3.8-5 libisl23_0.27-2 libitm1_16-20260425-1 libjansson4_2.14-2+b4 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_9.1.0-3 libjsoncpp26_1.9.7-2 libk5crypto3_1.22.1-2.1 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-2.1 libkrb5support0_1.22.1-2.1 liblapack-dev_3.12.1-7+b1 liblapack3_3.12.1-7+b1 libldap2_2.6.10+dfsg-1+b1 liblsan0_16-20260425-1 libltdl-dev_2.5.4-11 libltdl7_2.5.4-11 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.46-5+b2 libmagic1t64_1:5.46-5+b2 libmd0_1.1.0-2+b2 libmount1_2.42-6 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libmunge2_0.5.18-1 libmuparser-dev_2.3.4-2+b1 libmuparser2v5_2.3.4-2+b1 libncursesw6_6.6+20251231-1+b1 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp3-9_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-ossl0_1.22.1-1 libnl-3-200_3.12.0-2+b1 libnl-3-dev_3.12.0-2+b1 libnl-route-3-200_3.12.0-2+b1 libnl-route-3-dev_3.12.0-2+b1 libnuma-dev_2.0.19-1+b2 libnuma1_2.0.19-1+b2 libopenmpi-dev_5.0.10-1 libopenmpi40_5.0.10-1 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpciaccess0_0.17-3+b4 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-7+b1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpmix2t64_6.0.0+really5.0.9-3+b1 libproc2-0_2:4.0.4-9+b2 libprrte-bin_3.0.13-3 libprrte-dev_3.0.13-3 libprrte3_3.0.13-3 libpsl5t64_0.21.5-1 libpython3-dev_3.13.9-3+b1 libpython3-stdlib_3.13.9-3+b1 libpython3.13_3.13.12-1 libpython3.13-dev_3.13.12-1 libpython3.13-minimal_3.13.12-1 libpython3.13-stdlib_3.13.12-1 librdmacm1t64_63.0-1 libreadline8t64_8.3-4 librhash1_1.4.6-1.1+b1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libselinux1_3.10-1 libsframe3_2.46-3 libsmartcols1_2.42-6 libsqlite3-0_3.46.1-9+b1 libssh2-1t64_1.11.1-3 libssl3t64_3.6.2-1 libstdc++-15-dev_15.2.0-17 libstdc++6_16-20260425-1 libsystemd-shared_260.1-1 libsystemd0_260.1-1 libtinfo6_6.6+20251231-1+b1 libtool_2.5.4-11 libtsan2_16-20260425-1 libubsan1_16-20260425-1 libucc1_1.7.0~rc1-1 libuchardet0_0.0.8-2+b2 libucx0_1.20.1~rc2-1 libudev1_260.1-1 libunistring5_1.4.2-1 libuuid1_2.42-6 libuv1t64_1.51.0-2+b2 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libxau6_1:1.0.11-1+b2 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2+b1 libxext6_2:1.3.4-1+b4 libxml2-16_2.15.2+dfsg-0.1 libxnvctrl0_535.171.04-1+b3 libxxhash0_0.8.3-2+b2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.0.4-1 lsb-release_12.1-2 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 media-types_14.0.0 mount_2.42-6 mpi-default-bin_1.20 mpi-default-dev_1.20 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1+b1 netbase_6.5 ocl-icd-libopencl1_2.3.4-1+b1 openmpi-bin_5.0.10-1 openmpi-common_5.0.10-1 openssh-client_1:10.3p1-2 openssl-provider-legacy_3.6.2-1 patch_2.8-2 perl_5.40.1-7+b1 perl-base_5.40.1-7+b1 perl-modules-5.40_5.40.1-7 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 procps_2:4.0.4-9+b2 pybind11-dev_3.0.1-3 python3_3.13.9-3+b1 python3-dev_3.13.9-3+b1 python3-iniconfig_2.1.0-2 python3-minimal_3.13.9-3+b1 python3-mpi4py_4.1.1-9 python3-networkx_3.4.2-5 python3-numpy_1:2.4.4+ds-2 python3-numpy-dev_1:2.4.4+ds-2 python3-packaging_26.0-1 python3-pluggy_1.6.0-2 python3-pybind11_3.0.1-3 python3-pygments_2.19.2+dfsg-1 python3-pytest_9.0.3-1 python3.13_3.13.12-1 python3.13-dev_3.13.12-1 python3.13-minimal_3.13.12-1 readline-common_8.3-4 rpcsvc-proto_1.4.3-1+b2 sed_4.9-3 sensible-utils_0.0.26 systemd_260.1-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tzdata_2026b-1 util-linux_2.42-6 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Thu, 14 May 2026 23:18:43 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gromacs Binary: gromacs, gromacs-data, libgromacs11, libgromacs-dev, libnblib-gmx0, libnblib-gmx-dev Architecture: any all Version: 2026.2-2 Maintainer: Debichem Team Uploaders: Nicholas Breen Homepage: https://www.gromacs.org/ Standards-Version: 4.7.4 Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, mpi-default-bin, perl Build-Depends: architecture-is-64-bit, bash-completion, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, make (>= 4.4), mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev Build-Depends-Indep: doxygen, furo, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, rdfind, symlinks Package-List: gromacs deb science optional arch=any gromacs-data deb science optional arch=all libgromacs-dev deb libdevel optional arch=any libgromacs11 deb libs optional arch=any libnblib-gmx-dev deb libdevel optional arch=any libnblib-gmx0 deb libs optional arch=any Checksums-Sha1: 0f7ecbf91234135a7db353deae7e7cd4f8d834c7 16580813 gromacs_2026.2.orig-regressiontests.tar.gz 5d629a201623c2e152c162bff3b47caf036ee689 45943914 gromacs_2026.2.orig.tar.gz 1df4b0bc96e566aadce6181cb62797d1467155de 13658756 gromacs_2026.2-2.debian.tar.xz Checksums-Sha256: f5fe50134d01e0c961812537cbb8253a4bd06831b6e329144ddbb6ba22393a36 16580813 gromacs_2026.2.orig-regressiontests.tar.gz d27e4455e8246177952366798631a0dad9f2e1f567400a6cb854a168dcc050dd 45943914 gromacs_2026.2.orig.tar.gz 6ed2b4bea7dad0c87c0df14c99df6baa488c57ec196ce167f43729f1eb8ed1cb 13658756 gromacs_2026.2-2.debian.tar.xz Files: 074be6e754e7db6e89a1c78347a1d0ac 16580813 gromacs_2026.2.orig-regressiontests.tar.gz 74c859cb7f53919f9c7760c287b43323 45943914 gromacs_2026.2.orig.tar.gz 2e1719f57b6fc32504778008cd38a79f 13658756 gromacs_2026.2-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmoDSrwACgkQQc5/C58b izKf0Qf9FLYmgFsne5jWn5P2gqGcuQ8iFvhvN9IIBGqa4O3zFLCd1kPpAytvJZSk v7X8AOIz6eqymeItZgHprhpAl4pOIlZCLoYrBfmuzFQMptzClSSXNF55pkFAzuPQ Lsdic9QcDirsDoiF/USRbSDahpXOTZ1rjIP8+L7SVzWsef6L9i+bl9KBt0sqNIOw w9oc1SyT+v7vn5aOd0xyd3wxETFgf3Z6wUBjRvdhIRjjeBmhhtbifJLRz2INHkll m3ybxW1EGZm0cPXNl/XpbM555NCu6jJGu2ghC+H2eByaXQwCrlJeM0S2UHcAzyGv vdiKOuU1qaR9lgEhK84Af/UOz3Je8w== =aB+l -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./gromacs_2026.2-2.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./gromacs_2026.2-2.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting gromacs in /build/reproducible-path/gromacs-2026.2 dpkg-source: info: unpacking gromacs_2026.2.orig.tar.gz dpkg-source: info: unpacking gromacs_2026.2.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2026.2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying manual-local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying script-shebang-line.patch dpkg-source: info: applying threadmpi-tests.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1778600100 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2026.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh_testdir dh_testroot dh_clean build-basic build-mpi build-manual build/ py3clean admin docs debian/rules binary-arch dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/reproducible-path/gromacs-2026.2 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2026.2-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.12", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /lib/riscv64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/riscv64-linux-gnu/libz.so (found version "1.3.2") -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so - found -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - RISC-V 64 -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 0 -- Detected build CPU model - 0 -- Detected build CPU stepping - 0 -- Detected build CPU features - -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/riscv64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/riscv64-linux-gnu/liblapack.so;/usr/lib/riscv64-linux-gnu/libblas.so -- No image conversion possible without ImageMagick -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (46.1s) -- Generating done (2.5s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.2/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2026.2 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2026.2-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.12", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/riscv64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /lib/riscv64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/riscv64-linux-gnu/libz.so (found version "1.3.2") -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so - found -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - RISC-V 64 -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 0 -- Detected build CPU model - 0 -- Detected build CPU stepping - 0 -- Detected build CPU features - -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/riscv64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/riscv64-linux-gnu/liblapack.so;/usr/lib/riscv64-linux-gnu/libblas.so -- No image conversion possible without ImageMagick -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (43.5s) -- Generating done (2.4s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.2/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2026.2 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2026.2-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=None -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMXAPI=ON -DGMX_PYTHON_PACKAGE=ON) -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.12", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.10 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "_mpi" -- Using default library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /lib/riscv64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/riscv64-linux-gnu/libz.so (found version "1.3.2") -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so - found -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - RISC-V 64 -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 0 -- Detected build CPU model - 0 -- Detected build CPU stepping - 0 -- Detected build CPU features - -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3f.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/riscv64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/riscv64-linux-gnu/liblapack.so;/usr/lib/riscv64-linux-gnu/libblas.so -- No image conversion possible without ImageMagick -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO_AUTO -- Performing Test HAS_FLTO_AUTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2026.2/build/mpi/bin/gmx_mpi from build tree. -- Found pybind11: /usr/include (found version "3.0.1") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) Doxygen needs to be installed to generate the C++ documentation -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (48.2s) -- Generating done (2.4s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.2/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2026.2 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2026.2-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=None -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.13.12", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.10 -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST -- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success -- Performing Test HAS_WARNING_NO_CAST_QUAL -- Performing Test HAS_WARNING_NO_CAST_QUAL - Success -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE -- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Using default binary suffix: "_mpi_d" -- Using default library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /lib/riscv64-linux-gnu/libhwloc.so (found suitable version "2.12.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/riscv64-linux-gnu/libz.so (found version "1.3.2") -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/riscv64-linux-gnu/libz.so - found -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Torch not found. Neural network potential support will be disabled. -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - RISC-V 64 -- Detected build CPU brand - Unknown CPU brand -- Detected build CPU family - 0 -- Detected build CPU model - 0 -- Detected build CPU stepping - 0 -- Detected build CPU features - -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/riscv64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/riscv64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/riscv64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/riscv64-linux-gnu/liblapack.so;/usr/lib/riscv64-linux-gnu/libblas.so -- No image conversion possible without ImageMagick -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Looking for open_memstream -- Looking for open_memstream - found -- Looking for dlopen -- Looking for dlopen - found -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (Required is at least version "1.10.7") -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (44.6s) -- Generating done (2.4s) -- Build files have been written to: /build/reproducible-path/gromacs-2026.2/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j4 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.2 -B/build/reproducible-path/gromacs-2026.2/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.2/build/basic/CMakeFiles /build/reproducible-path/gromacs-2026.2/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/selection /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.2/build/basic/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" thread_mpi make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.2-Debian_2026.2_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.2 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.2/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.2/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2026.2-2 -P /build/reproducible-path/gromacs-2026.2/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr/xdr_array.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/pthreads.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/bcast.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast 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CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/reduce.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/merge_sort.c /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" lmfit_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/lmfit/lmmin.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat 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-o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/gather.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/scatter.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/topology.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/vals16.c /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvar.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 3%] Built target thread_mpi cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvar_neuralnetworkcompute.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/lib/tng_io.c [ 3%] Built target scanner cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmm_mdmodule.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmmforceproviderbuilder.cpp /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -DGMX_DESCRIBE_BLAS="External - detected on the system" -DGMX_DESCRIBE_LAPACK="External - detected on the system" -DGMX_FFT_MKL=0 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/binary_information.cpp.o -MF CMakeFiles/linearalgebra.dir/binary_information.cpp.o.d -o CMakeFiles/linearalgebra.dir/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/binary_information.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmoptions.cpp.o -MF CMakeFiles/fmm.dir/fmmoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmmoptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/gmx_arpack.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 5%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -MF CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmmforceprovider_stub.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/options /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/abstractoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 6%] Built target fmm cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/basicoptions.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 8%] Built target linearalgebra cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_abmd.cpp /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/h5md && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/h5md.cpp.o -MF CMakeFiles/h5md.dir/h5md.cpp.o.d -o CMakeFiles/h5md.dir/h5md.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/h5md/h5md.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 8%] Built target h5md cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 8%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/behaviorcollection.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/gmx.cpp /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/legacymodules.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 8%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/filenameoption.cpp /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_meta.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 8%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2026.2/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/optionsvisitor.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 8%] Built target pulling cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_distances.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 10%] Built target taskassignment cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include 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/build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security 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/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/src/include 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-fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 13%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 15%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2026.2/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2026.2/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include 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-isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include 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-isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ 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-isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include 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-Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ 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-Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem 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-I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include 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src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include 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/build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src 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/build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include 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/build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include 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/build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/gmxfio.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src 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CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 96%] Built target gmxapi cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include 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api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o /usr/lib/riscv64-linux-gnu/libm.so ../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 98%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/samples /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" methane-water-integration cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/samples /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/samples 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-I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now 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"CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2026.2/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.2/build/basic/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -j4 -C build/basic-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.2 -B/build/reproducible-path/gromacs-2026.2/build/basic-dp --check-build-system 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/build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/selection /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" thread_mpi make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.2-Debian_2026.2_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.2 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.2/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.2/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2026.2-2 -P /build/reproducible-path/gromacs-2026.2/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/parser.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr/xdr.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr/xdr_array.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/rpc_xdr && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr/xdr_stdio.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/pthreads.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 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CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/barrier.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/p2p_send_recv.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/reduce.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o 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cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/reduce_fast.cpp cd 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/usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/scatter.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/merge_sort.c /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/topology.cpp cd 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/usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 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-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC 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src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 1%] Built target thread_mpi /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm 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-I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmm_mdmodule.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmmforceproviderbuilder.cpp cd 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -DGMX_DESCRIBE_BLAS="External - detected on the system" -DGMX_DESCRIBE_LAPACK="External - detected on the system" -DGMX_FFT_MKL=0 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/binary_information.cpp.o -MF CMakeFiles/linearalgebra.dir/binary_information.cpp.o.d -o CMakeFiles/linearalgebra.dir/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/binary_information.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -MF CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 3%] Built target tng_io_obj /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/options /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/abstractoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 5%] Built target fmm cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 6%] Built target linearalgebra cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_abmd.cpp /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/h5md && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/h5md.cpp.o -MF CMakeFiles/h5md.dir/h5md.cpp.o.d -o CMakeFiles/h5md.dir/h5md.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/h5md/h5md.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 6%] Built target h5md cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 6%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_histogram.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/legacymodules.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 6%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/filenameoptionmanager.cpp /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_opes.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/treesupport.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 8%] Built target options cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_restraint.cpp /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pullutil.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 8%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_alchlambda.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 8%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/decidegpuusage.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include 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-c /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator/constraintelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 8%] Built target taskassignment cd 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/nr_jacobi.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 12%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 13%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2026.2/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2026.2/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" libgromacs make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/booltype.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include 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-isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include 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-isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include 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-isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include 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/build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_4x4.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_reference/kernel_ref_4x4.cpp cd 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC 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-I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include 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-fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/gpu_utils.cpp cd 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external 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/build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include 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/build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include 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-isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/print_validation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/print_validation.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include 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CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/libgromacs.dir/link.d -Wl,-soname,libgromacs_d.so.11 -o ../../lib/libgromacs_d.so.11.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /lib/riscv64-linux-gnu/libhwloc.so -lrt /usr/lib/riscv64-linux-gnu/libfftw3.so /usr/lib/riscv64-linux-gnu/libblas.so /usr/lib/riscv64-linux-gnu/liblapack.so /usr/lib/riscv64-linux-gnu/libblas.so /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/riscv64-linux-gnu/liblapack.so /usr/lib/riscv64-linux-gnu/libm.so -lm /usr/lib/riscv64-linux-gnu/libz.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 -ldl cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.11.0.0 ../../lib/libgromacs_d.so.11 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 94%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" gmx make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/gmxapi /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" gmxapi make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" nblib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/resourceassignment.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/context.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/box.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 94%] Built target gmx cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include 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api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include 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CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi.dir/link.d -Wl,-soname,libgmxapi_d.so.0 -o ../../lib/libgmxapi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_d.so.0.4.0 ../../lib/libgmxapi_d.so.0 ../../lib/libgmxapi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 96%] Built target gmxapi cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include 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CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib.dir/link.d -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o /usr/lib/riscv64-linux-gnu/libm.so ../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 98%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/samples /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" argon-forces-integration make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/samples /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" methane-water-integration make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2026.2/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2026.2/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.2/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -j4 -C build/basic tests make[1]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.2 -B/build/reproducible-path/gromacs-2026.2/build/basic --check-build-system 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'/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/external/googletest/googletest 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PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.2 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.2/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.2/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2026.2-2 -P /build/reproducible-path/gromacs-2026.2/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/googletest/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow 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Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 0%] Built target release-version-info /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/external/rpc_xdr 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CMakeFiles/mpithreads.dir/main.cpp.o.d -o CMakeFiles/mpithreads.dir/main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build.make src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT 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../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/sync_cyclecount make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 8%] Built target sync_cyclecount cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/once.cpp.o -MF CMakeFiles/mpithreads.dir/once.cpp.o.d -o CMakeFiles/mpithreads.dir/once.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/once.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o -MF CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/send_recv.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/send_recv.cpp /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build.make src/external/thread_mpi/test/CMakeFiles/notmpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test/CMakeFiles/notmpi.dir/DependInfo.cmake "--color=" notmpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build.make src/external/thread_mpi/test/CMakeFiles/notmpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/notmpi.dir/notmpi.cpp.o -MF CMakeFiles/notmpi.dir/notmpi.cpp.o.d -o CMakeFiles/notmpi.dir/notmpi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/notmpi.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/multicast.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/multicast.cpp.o -MF CMakeFiles/mpithreads.dir/multicast.cpp.o.d -o CMakeFiles/mpithreads.dir/multicast.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/multicast.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/notmpi.dir/link.txt --verbose=1 cd 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../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/mpi_speedtest make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 8%] Built target mpi_speedtest cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/cond-var.cpp.o -MF CMakeFiles/mpithreads.dir/cond-var.cpp.o.d -o CMakeFiles/mpithreads.dir/cond-var.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/cond-var.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/notmpi make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 8%] Built target notmpi /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/build.make src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/alloc_check.cpp.o -MF CMakeFiles/alloc_check.dir/alloc_check.cpp.o.d -o CMakeFiles/alloc_check.dir/alloc_check.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/alloc_check.cpp /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/atomic.cpp.o -MF CMakeFiles/mpithreads.dir/atomic.cpp.o.d -o CMakeFiles/mpithreads.dir/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/atomic.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/alloc_check.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis 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../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 8%] Built target taskassignment /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.2/build/basic 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CMakeFiles/mpithreads.dir/send_recv.cpp.o CMakeFiles/mpithreads.dir/multicast.cpp.o "CMakeFiles/mpithreads.dir/cond-var.cpp.o" CMakeFiles/mpithreads.dir/atomic.cpp.o CMakeFiles/mpithreads.dir/cycles.cpp.o CMakeFiles/mpithreads.dir/split.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o 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make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 60%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/gmxapi /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" gmxapi make[4]: 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../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 64%] Built target testutils-mpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem 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-Wl,--dependency-file=CMakeFiles/mpicomm-test.dir/link.d "CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o" "CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mpicomm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 64%] Built target mpicomm-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 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-DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem 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"CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 66%] Built target testutils-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include 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make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" awh-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd 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/build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests/awh_setup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o" "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 66%] Built target utility-mpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o -MF CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o.d -o CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/constraintgroupsize.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests/bias.cpp /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" density_fitting_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ 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-I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/expanded.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 66%] Built target density_fitting_applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include 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-isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests/friction_metric.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/langevin.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/langevintestdata.cpp /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" qmmm_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 66%] Built target awh-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" colvars_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. 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-I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" 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/build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/scope_guard.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/strconvert.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 67%] Built target qmmm_applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/shake.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 68%] Built target colvars_applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/template_mp.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/updategroups.cpp /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/DependInfo.cmake "--color=" plumed_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" plumed_md-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 68%] Built target plumed_applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/textreader.cpp /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" nnpot_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/vsite.cpp.o -MF CMakeFiles/mdlib-test.dir/vsite.cpp.o.d -o CMakeFiles/mdlib-test.dir/vsite.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/vsite.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/mdgpugraph.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_md-test.dir/link.d "CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o" "CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o" "CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/plumed_md-test ../../../../../lib/libtestutils.a ../../../../../lib/libmdrun_test_infrastructure.a -ldl ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 69%] Built target plumed_md-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/nnpot/tests/nnpottopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/wholemoleculetransform.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 69%] Built target applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" listed_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/txtdump.cpp.o -MF CMakeFiles/utility-test.dir/txtdump.cpp.o.d -o CMakeFiles/utility-test.dir/txtdump.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/txtdump.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/vsite.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 71%] Built target mdlib-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/typetraits.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" nbnxm-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/vecdump.cpp.o -MF CMakeFiles/utility-test.dir/vecdump.cpp.o.d -o CMakeFiles/utility-test.dir/vecdump.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/vecdump.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 71%] Built target nnpot_applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/vectypes.cpp.o -MF CMakeFiles/utility-test.dir/vectypes.cpp.o.d -o CMakeFiles/utility-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/vectypes.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" nbnxm-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem 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-DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/kernel_test.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/listed_forces/tests/pairs.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 72%] Built target nbnxm-gpu-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/kernelsetup.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" nonbonded-fep-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/freeenergykernel.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -MF CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o.d -o CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/plainpairlist.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 72%] Built target listed_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/DependInfo.cmake "--color=" nonbonded-fep-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/freeenergygpukernel.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/testsystem.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-gpu-test.dir/link.d "CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o" "CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 73%] Built target nonbonded-fep-gpu-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make 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'/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 73%] Built target nbnxm-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" domdec-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/domdec/tests/hashedmap.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 73%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" domdec-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/domdec/tests/haloexchange_mpi.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/mpicomm.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/txtdump.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/vecdump.cpp.o" "CMakeFiles/utility-test.dir/vectypes.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 75%] Built target utility-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 75%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2026.2/build/basic 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'/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" fft-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 75%] Built target domdec-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 75%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 75%] Built target fft-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" 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src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/device_availability.cpp /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem 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CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -MF CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/hostallocator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 75%] Built target ewald-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/typecasts.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/tests/fmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/tests/fmmforceproviderbuilder.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-mpi-test.dir/link.d "CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o" "CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 76%] Built target gpu_utils-mpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/hardware/tests/mockhardwaretopology.cpp /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" math-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fmm-interface-tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fmm-interface-tests.dir/link.d "CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o" "CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fmm-interface-tests ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 76%] Built target fmm-interface-tests cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" mdrunutility-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/complex.cpp.o -MF CMakeFiles/math-test.dir/complex.cpp.o.d -o CMakeFiles/math-test.dir/complex.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/complex.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" 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/build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 76%] Built target mdrunutility-test-shared cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 76%] Built target hardware-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem 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CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/exponentialmovingaverage.cpp /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" mdspan-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests/accessor_policy.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 76%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" mdtypes-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/enerdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/tests/enerdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/tests/observablesreducer.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" onlinehelp-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o 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../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 76%] Built target onlinehelp-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include 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src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include 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src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 77%] Built target mdspan-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include 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-I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/densityfittingforce.cpp /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" pbcutil-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/neldermead.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 78%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/optimization.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 78%] Built target mdtypes-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/paddedvector.cpp /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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-isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/normaldistribution.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" restraintpotential-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 78%] Built target restraintpotential-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/tabulatednormaldistribution.cpp /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/serialization/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/DependInfo.cmake "--color=" serialization-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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-DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/serialization/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/serialization-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/uniformintdistribution.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/serialization-test.dir/link.d "CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/serialization-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 78%] Built target serialization-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" table-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/tables/tests/splinetable.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 78%] Built target random-test cd 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/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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/usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 78%] Built target taskassignment-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" timing-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 78%] Built target table-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" topology-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/atoms.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 78%] Built target timing-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/tests/pull.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 80%] Built target math-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" simd-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/idef.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 80%] Built target pull-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/generate_test_points.cpp.o -MF CMakeFiles/simd-test.dir/generate_test_points.cpp.o.d -o CMakeFiles/simd-test.dir/generate_test_points.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/generate_test_points.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/index.cpp /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/compat/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/compat/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" compat-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 80%] Built target compat-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/symtab.cpp /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" gmxana-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -MF CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmxanatestbase.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd_floatingpoint_util.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 80%] Built target options-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd_math.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" gmxpreprocess-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/convparm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_rms.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_rmsf.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 81%] Built target topology-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" pdb2gmx1-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/generate_test_points.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 83%] Built target simd-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/genion.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" pdb2gmx2-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 84%] Built target gmxana-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" pdb2gmx3-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 84%] Built target pdb2gmx1-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 84%] Built target pdb2gmx2-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" correlations-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/correlationfunctions/tests/correlationdataset.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" analysisdata-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src 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src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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/lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 84%] Built target pdb2gmx3-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" coordinateio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/builder.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 84%] Built target correlations-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" energyanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/outputadapters.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 85%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" tool-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 85%] Built target analysisdata-test-shared /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/DependInfo.cmake "--color=" tool-test-with-leaks make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests/convert-tpr-with-leaks.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests/helpwriting.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 86%] Built target energyanalysis-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests/report_methods.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 86%] Built target tool-test-with-leaks /usr/bin/make -f src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/build.make src/gromacs/fileio/h5md/tests/CMakeFiles/h5md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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'/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" fileio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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-o CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests/trjconv.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/h5md/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/h5md-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast 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/lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 87%] Built target h5md-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include 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src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" selection-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 88%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" mdrun-output-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/compressed_x_output.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 88%] Built target tool-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/helpwriting.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" mdrun-modules-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/densityfittingmodule.cpp cd 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/timecontrol.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 88%] Built target mdrun-modules-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o -MF CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o.d -o CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/xdr_serializer.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 88%] Built target mdrun-output-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" mdrun-io-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 89%] Built target fileio-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests/toputils.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" mdrun-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/awh.cpp.o -MF CMakeFiles/mdrun-test.dir/awh.cpp.o.d -o CMakeFiles/mdrun-test.dir/awh.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/awh.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" mdrun-single-rank-algorithms-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src 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-DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/orires.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 89%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" minimize-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 89%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 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/build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/rerun.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 89%] Built target mdrun-io-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/constantacceleration.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 89%] Built target minimize-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" mdrun-tpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" mdrun-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 89%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" mdrun-multisim-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem 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CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/multisim.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 89%] Built target mdrun-non-integrator-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src 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-DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/awh.cpp.o" "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory 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-MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-equivalence-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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/build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 90%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make 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/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem 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CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 91%] Built target mdrun-multisim-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" mdrun-coordination-basic-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 91%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" mdrun-coordination-coupling-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 92%] Built target mdrun-mpi-pme-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" mdrun-coordination-constraints-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 92%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" mdrun-fep-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/expandedensemble.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 93%] Built target mdrun-coordination-coupling-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 93%] Built target mdrun-coordination-basic-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" mdrun-pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" mdrun-rotation-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 93%] Built target mdrun-coordination-constraints-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 93%] Built target mdrun-fep-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" mdrun-vsites-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f 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-DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem 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/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 94%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests/runner.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 94%] Built target mdrun-vsites-test cd /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests/status.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 94%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests/stopsignaler.cpp /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" workflow-details-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/workflow/tests/workflow.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" nblib-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/integrator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 95%] Built target workflow-details-test cd /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include 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api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/tpr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test 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api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/c++ 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api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/nbkernelsystem.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 96%] Built target nblib-tpr-test cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/topology.cpp /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" nblib-listed-forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/util/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/util/tests /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" nblib-util-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/util/tests/setup.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 96%] Built target nblib-integration-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include 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CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 96%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" mdrunutility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -MF CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests/plainpairlistranges.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 97%] Built target nblib-setup-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 97%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/shiftforces.cpp cd 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/pargs.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" mdrunutility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make 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-MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" analysisdata-test make[4]: 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 97%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/arraydata.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 98%] Built target commandline-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" trajectoryanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/histogram.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 98%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" nblib-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [ 98%] Built target nblib-tests cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT 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-I/build/reproducible-path/gromacs-2026.2/build/basic/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 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"CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' cd /build/reproducible-path/gromacs-2026.2/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic /build/reproducible-path/gromacs-2026.2/build/basic/CMakeFiles/tests.dir/DependInfo.cmake "--color=" tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.2/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2026.2/build/basic/lib ctest -V -E MdlibUnitTest) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2026.2/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2026.2/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2026.2/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 1827378687 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.016 0.008 197.7 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 60.972 0.394 2.768 0.003 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (959 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -548540929 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.028 0.014 198.6 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 36.497 0.658 4.624 0.002 1: [ OK ] GmxApiTest.RunnerBasicMD (903 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -541067653 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.088 0.044 199.6 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 80.782 0.297 2.089 0.004 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.035 0.018 199.0 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 198.963 0.121 0.848 0.009 1: [ OK ] GmxApiTest.RunnerReinitialize (926 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -378838313 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.087 0.043 199.5 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 11.674 2.056 14.455 0.001 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.013 0.006 198.3 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 78.428 0.306 2.152 0.004 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (908 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to 1602219260 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.087 0.044 199.5 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 19.394 1.238 8.701 0.001 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.013 0.007 197.2 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 49.860 0.481 3.384 0.002 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (921 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -1216676417 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (829 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (5450 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (5475 ms total) 1: [ PASSED ] 9 tests. 1/103 Test #1: GmxapiExternalInterfaceTests .............. Passed 5.56 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -136388690 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (821 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -138412871 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (795 ms) 2: [----------] 2 tests from GmxApiTest (1617 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (1633 ms total) 2: [ PASSED ] 2 tests. 2/103 Test #2: GmxapiInternalInterfaceTests .............. Passed 1.66 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (36 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (30 ms) 3: [----------] 8 tests from NBlibTest (68 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (2 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (1 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (2 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (0 ms) 3: [----------] 1 test from LinearChainDataFixture (0 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (78 ms total) 3: [ PASSED ] 44 tests. 3/103 Test #3: NbLibListedForcesTests .................... Passed 0.11 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/103 Test #4: NbLibSamplesTestArgon ..................... Passed 0.03 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358398 y 5.324894 z -80.600098 5/103 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.03 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (1 ms total) 6: [ PASSED ] 16 tests. 6/103 Test #6: NbLibUtilTests ............................ Passed 0.03 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (1 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (4 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (5 ms total) 7: [ PASSED ] 57 tests. 7/103 Test #7: NbLibSetupTests ........................... Passed 0.05 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (11 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (11 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (10 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (10 ms) 8: [----------] 4 tests from TprReaderTest (43 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (59 ms total) 8: [ PASSED ] 4 tests. 8/103 Test #8: NbLibTprTests ............................. Passed 0.09 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (1 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (1 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (10 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (10 ms total) 9: [ PASSED ] 20 tests. 9/103 Test #9: NbLibIntegrationTests ..................... Passed 0.04 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/103 Test #10: NbLibIntegratorTests ...................... Passed 0.03 sec test 11 Start 11: threadMPI-mpithreads 11: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mpithreads "-nt" "3" 11: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test 11: Test timeout computed to be: 1500 11: 11: thread_mpi tester. 11: 11: Number of threads: 3 11: 11: thread 0: got arg 10; total number of hw threads: 4 11: thread 1: got arg 10; total number of hw threads: 4 11: my rank = 0 11: thread 2: got arg 10; total number of hw threads: 4 11: my rank = 2 11: Setting thread affinity 11: my rank = 1 11: Testing atomic functions.. 11: OK. 11: Starting tMPI_Thread_cond_signal test: 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 1: 606 11: processed by thread 2: 394 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 443 11: processed by thread 2: 557 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 412 11: processed by thread 1: 588 11: 11: Starting tMPI_Thread_cond_broadcast test: 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 1: 836 11: processed by thread 2: 1164 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 909 11: processed by thread 2: 1091 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 869 11: processed by thread 1: 1131 11: 11: 11: sizeof(atomic_t) = 4, sizeof(atomic_t_ptr)=8, sizeof(spinlock)=4 11: Testing spinlocks.. 11: OK. 11: 11: Testing locks.. 11: OK. 11: 11: Barrier data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Starting MPI_Send and MPI_Recv tests 11: Received: 'From thread 1 to 0: hello.' 11: Received: 'From thread 2 to 0: hello.' 11: Received: 'From thread 1 to 1: hello.' 11: Received: 'From thread 2 to 1: hello.' 11: 11: Starting MPI_Sendrecv tests 11: Received: 'Sendrecv hello, from thread 1' 11: Received: 'Sendrecv hello, from thread 2' 11: Received: 'Sendrecv hello, from thread 0' 11: 11: Starting MPI_Isend/MPI_Irecv tests 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Split test 11: I'm in world rank 2, and have new rank 0 in group 0x7fff98005c00 of size 2 11: I'm in world rank 1, and have new rank 0 in group 0x7fff980061b0 of size 1 11: I'm in world rank 0, and have new rank 1 in group 0x7fff98005c00 of size 2 11: 11: Starting MPI_Split test 11: I'm in world rank 2, and have new rank 0 in group 0x7fff98006b90 of size 1 11: my rank is 2, MPI_Comm_compare said: 3 11: I'm in world rank 1, and have new rank 0 in group 0x7fff98006860 of size 1 11: my rank is 1, MPI_Comm_compare said: 3 11: I'm in world rank 0, and have new rank 0 in group 0x7fff980065f0 of size 1 11: my rank is 0, MPI_Comm_compare said: 3 11: 11: Starting MPI_Split test 11: I'm in world rank 2, and have new rank 0 in group 0x7fff98006b90 of size 3 11: my rank is 2, MPI_Comm_compare said: 2 11: I'm in world rank 1, and have new rank 1 in group 0x7fff98006b90 of size 3 11: my rank is 1, MPI_Comm_compare said: 2 11: I'm in world rank 0, and have new rank 2 in group 0x7fff98006b90 of size 3 11: my rank is 0, MPI_Comm_compare said: 2 11: Starting repeated MPI_Split() test. 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: Done. 11: 11: Starting MPI_Bcast test 11: Received: 'Broadcast message 0 from 0' 11: Received: 'Broadcast message 0 from 1' 11: Received: 'Broadcast message 0 from 2' 11: Received: 'Broadcast message 1 from 0' 11: Received: 'Broadcast message 1 from 1' 11: Received: 'Broadcast message 1 from 2' 11: Broadcast data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Gather test 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Gather data test: 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Gatherv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Scatter test 11: Received from 0: 'Scatter message from 000 to 000' 11: Received back from 1: 'Scatter message from 000 to 001' 11: Received back from 2: 'Scatter message from 000 to 002' 11: Scatter data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Scatterv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Alltoall test 11: From 0: 0->0(0) 1->0(0) 2->0(0) 11: From 1: 0->1(0) 1->1(0) 2->1(0) 11: From 2: 0->2(0) 1->2(0) 2->2(0) 11: From 0: 0->0(1) 1->0(1) 2->0(1) 11: From 1: 0->1(1) 1->1(1) 2->1(1) 11: From 2: 0->2(1) 1->2(1) 2->2(1) 11: From 0: 0->0(2) 1->0(2) 2->0(2) 11: From 1: 0->1(2) 1->1(2) 2->1(2) 11: From 2: 0->2(2) 1->2(2) 2->2(2) 11: From 0: 0->0(3) 1->0(3) 2->0(3) 11: From 1: 0->1(3) 1->1(3) 2->1(3) 11: From 2: 0->2(3) 1->2(3) 2->2(3) 11: Alltoallv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Reduce test 11: again: my rank = 0 11: Results from mpi_reduce: 11: (0: 2 == 2): OK 11: (1: 5 == 5): OK 11: (2: 8 == 8): OK 11: (3: 11 == 11): OK 11: (4: 14 == 14): OK 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 1 11: again: my rank = 2 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 1: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 2: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: again: my rank = 2 11: again: my rank = 0 11: again: my rank = 1 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 1: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 2: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 2 11: again: my rank = 0 11: again: my rank = 1 11: 11: Starting tMPI_Scan test 11: Results from mpi_scan process 0: 11: OK 11: again: my rank = 0 11: again: my rank = 2 11: again: my rank = 1 11: 11: Starting tMPI_Once test 11: Printing this number once: 0 (my rank=1) 11: Printing this number once: 2 (my rank=0) 11: Printing this number once: 3 (my rank=0) 11: Printing this number once: 4 (my rank=0) 11: Printing this number once: 5 (my rank=0) 11: Printing this number once: 6 (my rank=0) 11: Printing this number once: 7 (my rank=0) 11: I was first for 0, my rank=1 11: Printing this number once: 1 (my rank=2) 11: Printing this number once: 9 (my rank=1) 11: Printing this number once: 8 (my rank=0) 11: Done. 11: 11: Finishing.. 11/103 Test #11: threadMPI-mpithreads ...................... Passed 14.96 sec test 12 Start 12: threadMPI-sync_cyclecount 12: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/sync_cyclecount "2" "0" "1" 12: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test 12: Test timeout computed to be: 1500 12: 12: sync_cyclecount. 12: 12: Number of threads: 3 12: 12: Number of counters: 3 12: 12: No cycle count. 12/103 Test #12: threadMPI-sync_cyclecount ................. Passed 0.00 sec test 13 Start 13: threadMPI-mpi_speedtest 13: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mpi_speedtest "-nt" "3" 13: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test 13: Test timeout computed to be: 1500 13: No cycle count. 13: No cycle count. 13: No cycle count. 13/103 Test #13: threadMPI-mpi_speedtest ................... Passed 0.00 sec test 14 Start 14: threadMPI-notmpi 14: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/notmpi "-nt" "3" 14: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test 14: Test timeout computed to be: 1500 14: 14: notmpi. 14: 14: Number of threads: 3 14: 14: This platform supports setting thread affinity 14: My ID=1, i=1000, tid=0x7fffac000be0 14: My ID=0, i=1000, tid=0x5555abb2f5d0 14: My ID=2, i=1000, tid=0x7fffa4000be0 14: Total count: 3000 14/103 Test #14: threadMPI-notmpi .......................... Passed 0.01 sec test 15 Start 15: threadMPI-alloc_check 15: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/alloc_check "-nt" "3" 15: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/external/thread_mpi/test 15: Test timeout computed to be: 1500 15: 15: Memory (de)allocation tester. 15: 15: Number of threads: 3 15: 15: thread 0: got arg 10; total number of hw threads: 4 15: my rank = 0 15: thread 2: got arg 10; total number of hw threads: 4 15: my rank = 2 15: thread 1: got arg 10; total number of hw threads: 4 15: my rank = 1 15: 15: Starting MPI_Sendrecv tests 15: Received: 'Sendrecv hello, from thread 1' 15: Received: 'Sendrecv hello, from thread 2' 15: Received: 'Sendrecv hello, from thread 0' 15: 15: Starting MPI_Bcast test 15: Received: 'Broadcast message 0 from 0' 15: Received: 'Broadcast message 0 from 1' 15: Received: 'Broadcast message 0 from 2' 15: Received: 'Broadcast message 1 from 0' 15: Received: 'Broadcast message 1 from 1' 15: Received: 'Broadcast message 1 from 2' 15: 15: Starting MPI_Gather test 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Finishing.. 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15/103 Test #15: threadMPI-alloc_check ..................... Passed 0.00 sec test 16 Start 16: TestUtilsUnitTests 16: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/testutils/tests 16: Test timeout computed to be: 30 16: [==========] Running 81 tests from 8 test suites. 16: [----------] Global test environment set-up. 16: [----------] 10 tests from InteractiveTestHelperTest 16: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 16: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (1 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 16: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 16: [----------] 10 tests from InteractiveTestHelperTest (4 ms total) 16: 16: [----------] 10 tests from NameOfTestFromTupleTest 16: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 16: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 16: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 16: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 16: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 16: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 16: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 16: 16: [----------] 3 tests from RefDataFilenameMakerTest 16: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 16: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 16: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 16: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 16: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 16: 16: [----------] 6 tests from PosixMemstreamTest 16: [ RUN ] PosixMemstreamTest.ConstructsAndDestructs 16: [ OK ] PosixMemstreamTest.ConstructsAndDestructs (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilClosed 16: [ OK ] PosixMemstreamTest.HasAStreamUntilClosed (0 ms) 16: [ RUN ] PosixMemstreamTest.CanFetchString 16: [ OK ] PosixMemstreamTest.CanFetchString (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilStringIsFetched 16: [ OK ] PosixMemstreamTest.HasAStreamUntilStringIsFetched (0 ms) 16: [ RUN ] PosixMemstreamTest.CanWriteToStream 16: [ OK ] PosixMemstreamTest.CanWriteToStream (0 ms) 16: [ RUN ] PosixMemstreamTest.CanCheckBufferWithContents 16: [ OK ] PosixMemstreamTest.CanCheckBufferWithContents (0 ms) 16: [----------] 6 tests from PosixMemstreamTest (0 ms total) 16: 16: [----------] 37 tests from ReferenceDataTest 16: [ RUN ] ReferenceDataTest.HandlesSimpleData 16: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 16: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 16: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringBlockData 16: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesVectorData 16: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceData 16: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectData 16: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 16: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingData 16: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedData 16: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnys 16: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 16: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 16: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 16: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 16: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 16: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 16: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 16: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 16: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesReadingValues 16: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 16: [----------] 37 tests from ReferenceDataTest (11 ms total) 16: 16: [----------] 7 tests from FloatingPointDifferenceTest 16: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 16: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 16: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 16: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 16: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 16: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 16: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 16: 16: [----------] 4 tests from FloatingPointToleranceTest 16: [ RUN ] FloatingPointToleranceTest.UlpTolerance 16: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 16: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 16: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 16: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 16: 16: [----------] 4 tests from XvgTests 16: [ RUN ] XvgTests.CreateFile 16: [ OK ] XvgTests.CreateFile (0 ms) 16: [ RUN ] XvgTests.CheckMissing 16: [ OK ] XvgTests.CheckMissing (0 ms) 16: [ RUN ] XvgTests.CheckExtra 16: [ OK ] XvgTests.CheckExtra (0 ms) 16: [ RUN ] XvgTests.ReadIncorrect 16: [ OK ] XvgTests.ReadIncorrect (0 ms) 16: [----------] 4 tests from XvgTests (2 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 81 tests from 8 test suites ran. (20 ms total) 16: [ PASSED ] 81 tests. 16/103 Test #16: TestUtilsUnitTests ........................ Passed 0.05 sec test 17 Start 17: TestUtilsMpiUnitTests 17: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/testutils/tests 17: Test timeout computed to be: 30 17: [==========] Running 3 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 1 test from MpiSelfTest 17: [ RUN ] MpiSelfTest.Runs 17: [ OK ] MpiSelfTest.Runs (1 ms) 17: [----------] 1 test from MpiSelfTest (1 ms total) 17: 17: [----------] 2 tests from MpiRefDataTest 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank (1 ms) 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName (0 ms) 17: [----------] 2 tests from MpiRefDataTest (1 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 3 tests from 2 test suites ran. (3 ms total) 17: [ PASSED ] 3 tests. 17/103 Test #17: TestUtilsMpiUnitTests ..................... Passed 0.03 sec test 18 Start 18: UtilityUnitTests 18: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/UtilityUnitTests.xml" 18: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests 18: Test timeout computed to be: 30 18: [==========] Running 495 tests from 68 test suites. 18: [----------] Global test environment set-up. 18: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/0.Comparison 18: [ OK ] AllocatorTest/0.Comparison (0 ms) 18: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.Move 18: [ OK ] AllocatorTest/0.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/0 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/1.Comparison 18: [ OK ] AllocatorTest/1.Comparison (0 ms) 18: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.Move 18: [ OK ] AllocatorTest/1.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/1 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/2.Comparison 18: [ OK ] AllocatorTest/2.Comparison (0 ms) 18: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.Move 18: [ OK ] AllocatorTest/2.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/2 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/3.Comparison 18: [ OK ] AllocatorTest/3.Comparison (0 ms) 18: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.Move 18: [ OK ] AllocatorTest/3.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/3 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/4.Comparison 18: [ OK ] AllocatorTest/4.Comparison (0 ms) 18: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.Move 18: [ OK ] AllocatorTest/4.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/4 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator,gmx::PageAlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/5.Comparison 18: [ OK ] AllocatorTest/5.Comparison (0 ms) 18: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.Move 18: [ OK ] AllocatorTest/5.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/5 (0 ms total) 18: 18: [----------] 1 test from AllocatorUntypedTest 18: [ RUN ] AllocatorUntypedTest.Comparison 18: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 18: [----------] 1 test from AllocatorUntypedTest (0 ms total) 18: 18: [----------] 4 tests from EmptyArrayRefTest 18: [ RUN ] EmptyArrayRefTest.IsEmpty 18: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 18: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 18: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 18: 18: [----------] 1 test from EmptyConstArrayRefTest 18: [ RUN ] EmptyConstArrayRefTest.IsEmpty 18: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 18: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 18: 18: [----------] 8 tests from BoolType 18: [ RUN ] BoolType.ImplicitConversion 18: [ OK ] BoolType.ImplicitConversion (0 ms) 18: [ RUN ] BoolType.FalseByDefault 18: [ OK ] BoolType.FalseByDefault (0 ms) 18: [ RUN ] BoolType.Assignment 18: [ OK ] BoolType.Assignment (0 ms) 18: [ RUN ] BoolType.Copy 18: [ OK ] BoolType.Copy (0 ms) 18: [ RUN ] BoolType.ArrayRefCanBeCreated 18: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 18: [ RUN ] BoolType.CanBeCastToBool 18: [ OK ] BoolType.CanBeCastToBool (0 ms) 18: [ RUN ] BoolType.HasSizeOfBool 18: [ OK ] BoolType.HasSizeOfBool (0 ms) 18: [ RUN ] BoolType.HasAlignmentOfBool 18: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 18: [----------] 8 tests from BoolType (0 ms total) 18: 18: [----------] 4 tests from ArrayRefFromBoolTypeVector 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.Works 18: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 18: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 18: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 18: 18: [----------] 7 tests from CStringUtilityTest 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 18: [ RUN ] CStringUtilityTest.strip_comment 18: [ OK ] CStringUtilityTest.strip_comment (0 ms) 18: [ RUN ] CStringUtilityTest.upstring 18: [ OK ] CStringUtilityTest.upstring (0 ms) 18: [ RUN ] CStringUtilityTest.ltrim 18: [ OK ] CStringUtilityTest.ltrim (0 ms) 18: [ RUN ] CStringUtilityTest.rtrim 18: [ OK ] CStringUtilityTest.rtrim (0 ms) 18: [ RUN ] CStringUtilityTest.trim 18: [ OK ] CStringUtilityTest.trim (0 ms) 18: [----------] 7 tests from CStringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from DefaultInitializationAllocator 18: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 18: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 18: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 18: 18: [----------] 4 tests from EnumerationHelpersTest 18: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 18: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 18: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 18: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 18: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 18: 18: [----------] 1 test from EnumClassSuitsEnumerationArray 18: [ RUN ] EnumClassSuitsEnumerationArray.Works 18: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 18: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 18: 18: [----------] 18 tests from FixedCapacityVectorTest 18: [ RUN ] FixedCapacityVectorTest.IsEmpty 18: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 18: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PushWorks 18: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PopWorks 18: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ResizeWorks 18: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ClearWorks 18: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 18: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.AtThrows 18: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 18: [ RUN ] FixedCapacityVectorTest.IteratorWorks 18: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 18: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 18: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 18: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 18: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.DataWorks 18: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 18: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 18: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 18: 18: [----------] 7 tests from TreeValueTransformTest 18: [ RUN ] TreeValueTransformTest.SimpleTransforms 18: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 18: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (3 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 18: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromString 18: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 18: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 18: [ RUN ] TreeValueTransformTest.ScopedTransformRules 18: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 18: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 18: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 18: [----------] 7 tests from TreeValueTransformTest (7 ms total) 18: 18: [----------] 1 test from TreeValueTransformErrorTest 18: [ RUN ] TreeValueTransformErrorTest.ConversionError 18: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 18: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 18: 18: [----------] 9 tests from ListOfLists 18: [ RUN ] ListOfLists.EmptyListOfListsWorks 18: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 18: [ RUN ] ListOfLists.AppendWorks 18: [ OK ] ListOfLists.AppendWorks (0 ms) 18: [ RUN ] ListOfLists.EmptyListWorks 18: [ OK ] ListOfLists.EmptyListWorks (0 ms) 18: [ RUN ] ListOfLists.AppendAccessWorks 18: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 18: [ RUN ] ListOfLists.ClearWorks 18: [ OK ] ListOfLists.ClearWorks (0 ms) 18: [ RUN ] ListOfLists.OutOfRangeAccessThrows 18: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 18: [ RUN ] ListOfLists.FrontAndBackWork 18: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 18: [ RUN ] ListOfLists.ExtractsAndRestores 18: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 18: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 18: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 18: [----------] 9 tests from ListOfLists (0 ms total) 18: 18: [----------] 7 tests from LoggerTest 18: [ RUN ] LoggerTest.EmptyLoggerWorks 18: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToStream 18: [ OK ] LoggerTest.LogsToStream (0 ms) 18: [ RUN ] LoggerTest.LogsToFile 18: [ OK ] LoggerTest.LogsToFile (0 ms) 18: [ RUN ] LoggerTest.LevelFilteringWorks 18: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleStreams 18: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleFiles 18: [ OK ] LoggerTest.LogsToMultipleFiles (1 ms) 18: [ RUN ] LoggerTest.LogsToStreamAndFile 18: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 18: [----------] 7 tests from LoggerTest (4 ms total) 18: 18: [----------] 7 tests from MessageStringCollectorTest 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 18: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 18: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveAssign 18: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 18: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 18: 18: [----------] 12 tests from MpiComm 18: [ RUN ] MpiComm.SingleRankNoComm 18: [ OK ] MpiComm.SingleRankNoComm (0 ms) 18: [ RUN ] MpiComm.CommWorld 18: [ OK ] MpiComm.CommWorld (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: ./src/gromacs/utility/tests/mpicomm.cpp:160: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:168: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:181: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:194: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (0 ms) 18: [ RUN ] MpiComm.ConstructorThrowsOnNull 18: ./src/gromacs/utility/tests/mpicomm.cpp:206: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull (0 ms) 18: [ RUN ] MpiComm.CopyConstructorWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:220: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CopyConstructorWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:243: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:259: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:281: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:298: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf (0 ms) 18: [----------] 12 tests from MpiComm (0 ms total) 18: 18: [----------] 1 test from PathTest 18: [ RUN ] PathTest.StripSourcePrefixWorks 18: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 18: [----------] 1 test from PathTest (0 ms total) 18: 18: [----------] 2 tests from PhysicalNodeCommunicatorTest 18: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 18: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 18: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 18: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 18: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 18: 18: [----------] 5 tests from Range 18: [ RUN ] Range.EmptyRangeWorks 18: [ OK ] Range.EmptyRangeWorks (0 ms) 18: [ RUN ] Range.NonEmptyRangeWorks 18: [ OK ] Range.NonEmptyRangeWorks (0 ms) 18: [ RUN ] Range.BeginEnd 18: [ OK ] Range.BeginEnd (0 ms) 18: [ RUN ] Range.IsInRangeWorks 18: [ OK ] Range.IsInRangeWorks (0 ms) 18: [ RUN ] Range.IteratorWorks 18: [ OK ] Range.IteratorWorks (0 ms) 18: [----------] 5 tests from Range (0 ms total) 18: 18: [----------] 3 tests from ScopeGuardTest 18: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 18: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 18: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 18: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 18: [----------] 3 tests from ScopeGuardTest (0 ms total) 18: 18: [----------] 7 tests from StringConvert 18: [ RUN ] StringConvert.NoResultFromEptyString 18: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 18: [ RUN ] StringConvert.ThreeFloatsSuccessfully 18: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 18: [ RUN ] StringConvert.OneIntSucessfully 18: [ OK ] StringConvert.OneIntSucessfully (0 ms) 18: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 18: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 18: [ RUN ] StringConvert.ThrowsWhenWrongSize 18: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 18: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 18: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 18: [----------] 7 tests from StringConvert (0 ms total) 18: 18: [----------] 7 tests from StringToEnumValueConverterTest 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 18: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 18: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 18: 18: [----------] 9 tests from StringUtilityTest 18: [ RUN ] StringUtilityTest.StartsWith 18: [ OK ] StringUtilityTest.StartsWith (0 ms) 18: [ RUN ] StringUtilityTest.EndsWith 18: [ OK ] StringUtilityTest.EndsWith (0 ms) 18: [ RUN ] StringUtilityTest.StripSuffixIfPresent 18: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 18: [ RUN ] StringUtilityTest.StripString 18: [ OK ] StringUtilityTest.StripString (0 ms) 18: [ RUN ] StringUtilityTest.SplitString 18: [ OK ] StringUtilityTest.SplitString (0 ms) 18: [ RUN ] StringUtilityTest.SplitDelimitedString 18: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 18: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 18: [----------] 9 tests from StringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from FormatStringTest 18: [ RUN ] FormatStringTest.HandlesBasicFormatting 18: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 18: [ RUN ] FormatStringTest.HandlesLongStrings 18: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 18: [----------] 2 tests from FormatStringTest (0 ms total) 18: 18: [----------] 1 test from StringFormatterTest 18: [ RUN ] StringFormatterTest.HandlesBasicFormatting 18: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 18: [----------] 1 test from StringFormatterTest (0 ms total) 18: 18: [----------] 1 test from formatAndJoinTest 18: [ RUN ] formatAndJoinTest.Works 18: [ OK ] formatAndJoinTest.Works (0 ms) 18: [----------] 1 test from formatAndJoinTest (0 ms total) 18: 18: [----------] 1 test from JoinStringsTest 18: [ RUN ] JoinStringsTest.Works 18: [ OK ] JoinStringsTest.Works (0 ms) 18: [----------] 1 test from JoinStringsTest (0 ms total) 18: 18: [----------] 6 tests from ReplaceAllTest 18: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 18: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesNoMatches 18: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 18: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 18: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 18: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 18: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 18: [----------] 6 tests from ReplaceAllTest (0 ms total) 18: 18: [----------] 10 tests from TextLineWrapperTest 18: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 18: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 18: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 18: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectly 18: [ OK ] TextLineWrapperTest.WrapsCorrectly (2 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndent 18: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 18: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 18: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 18: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 18: [----------] 10 tests from TextLineWrapperTest (4 ms total) 18: 18: [----------] 1 test from PrettyPrintListAsRangeTest 18: [ RUN ] PrettyPrintListAsRangeTest.Works 18: [ OK ] PrettyPrintListAsRangeTest.Works (0 ms) 18: [----------] 1 test from PrettyPrintListAsRangeTest (0 ms total) 18: 18: [----------] 1 test from CompileTimeStringJoin 18: [ RUN ] CompileTimeStringJoin.Works 18: [ OK ] CompileTimeStringJoin.Works (0 ms) 18: [----------] 1 test from CompileTimeStringJoin (0 ms total) 18: 18: [----------] 3 tests from TemplateMPTest 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 18: [----------] 3 tests from TemplateMPTest (0 ms total) 18: 18: [----------] 8 tests from TextWriterTest 18: [ RUN ] TextWriterTest.WritesLines 18: [ OK ] TextWriterTest.WritesLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInParts 18: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 18: [ RUN ] TextWriterTest.WritesWrappedLines 18: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 18: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 18: [ RUN ] TextWriterTest.TracksNewlines 18: [ OK ] TextWriterTest.TracksNewlines (0 ms) 18: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 18: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 18: [ RUN ] TextWriterTest.WritesIndentedLines 18: [ OK ] TextWriterTest.WritesIndentedLines (0 ms) 18: [ RUN ] TextWriterTest.ScopedIndenterWritesIndentedLines 18: [ OK ] TextWriterTest.ScopedIndenterWritesIndentedLines (0 ms) 18: [----------] 8 tests from TextWriterTest (3 ms total) 18: 18: [----------] 4 tests from DumpingTextTest 18: [ RUN ] DumpingTextTest.LegacyIndentingWorks 18: [ OK ] DumpingTextTest.LegacyIndentingWorks (0 ms) 18: [ RUN ] DumpingTextTest.ReportsWhenNotAvailableIdentically 18: [ OK ] DumpingTextTest.ReportsWhenNotAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.QuietWhenAvailableIdentically 18: [ OK ] DumpingTextTest.QuietWhenAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.PrintsTitleAndSizeIdentically 18: [ OK ] DumpingTextTest.PrintsTitleAndSizeIdentically (0 ms) 18: [----------] 4 tests from DumpingTextTest (1 ms total) 18: 18: [----------] 1 test from TypeTraitsTest 18: [ RUN ] TypeTraitsTest.IsIntegralConstant 18: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 18: [----------] 1 test from TypeTraitsTest (0 ms total) 18: 18: [----------] 41 tests from RVecTest 18: [ RUN ] RVecTest.CanBeStoredInVector 18: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAsMutable_rvec 18: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Array 18: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 18: [ RUN ] RVecTest.ComparesEqual 18: [ OK ] RVecTest.ComparesEqual (0 ms) 18: [ RUN ] RVecTest.ComparesUnequal 18: [ OK ] RVecTest.ComparesUnequal (0 ms) 18: [ RUN ] RVecTest.CanAddRVecToRvec 18: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanAddAssignRVecToRvec 18: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractRVecFromRvec 18: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 18: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanDotProductRVecByRvec 18: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanCrossProductRVecByRvec 18: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVecInplace 18: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 18: [ RUN ] RVecTest.CanScaleRVec 18: [ OK ] RVecTest.CanScaleRVec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVec 18: [ OK ] RVecTest.CanDivideRVec (0 ms) 18: [ RUN ] RVecTest.CanDoUnitvFromRVec 18: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanSqLengthOfRVec 18: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanLengthOfRVec 18: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToRVec 18: [ OK ] RVecTest.CanCastToRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToDVec 18: [ OK ] RVecTest.CanCastToDVec (0 ms) 18: [ RUN ] RVecTest.CanLeftScalarMultiply 18: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanRightScalarMultiply 18: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanGetUnitvFromRVec 18: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanGetSqLengthOfRVec 18: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanGetLengthOfRVec 18: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoCrossProductOfRVec 18: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoDotProductOfRVec 18: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanScaleByVector 18: [ OK ] RVecTest.CanScaleByVector (0 ms) 18: [ RUN ] RVecTest.CanNegate 18: [ OK ] RVecTest.CanNegate (0 ms) 18: [ RUN ] RVecTest.asIVec 18: [ OK ] RVecTest.asIVec (0 ms) 18: [ RUN ] RVecTest.elementWiseMin 18: [ OK ] RVecTest.elementWiseMin (0 ms) 18: [ RUN ] RVecTest.elementWiseMax 18: [ OK ] RVecTest.elementWiseMax (0 ms) 18: [ RUN ] RVecTest.WorksAs_dvec_Reference 18: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_ivec_Reference 18: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Reference 18: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 18: [ RUN ] RVecTest.CopyConstructorWorks 18: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 18: [ RUN ] RVecTest.CopyAssignmentWorks 18: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.MoveConstructorWorks 18: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 18: [ RUN ] RVecTest.MoveAssignmentWorks 18: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.UsableInConstexpr 18: [ OK ] RVecTest.UsableInConstexpr (0 ms) 18: [----------] 41 tests from RVecTest (0 ms total) 18: 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 18: 18: [----------] 11 tests from WithInputPaths/PathSearchTest 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 18: [----------] 11 tests from WithInputPaths/PathSearchTest (5 ms total) 18: 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 18: 18: [----------] 24 tests from Works/DumpingVectorsTest 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 (0 ms) 18: [----------] 24 tests from Works/DumpingVectorsTest (8 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 495 tests from 68 test suites ran. (44 ms total) 18: [ PASSED ] 485 tests. 18: [ SKIPPED ] 10 tests, listed below: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull 18: [ SKIPPED ] MpiComm.CopyConstructorWorks 18: [ SKIPPED ] MpiComm.AssigmentWorks 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf 18: 18: YOU HAVE 1 DISABLED TEST 18: 18/103 Test #18: UtilityUnitTests .......................... Passed 0.10 sec test 19 Start 19: MpiCommTests 19: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mpicomm-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MpiCommTests.xml" 19: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests 19: Test timeout computed to be: 30 19: [==========] Running 12 tests from 1 test suite. 19: [----------] Global test environment set-up. 19: [----------] 12 tests from MpiComm 19: [ RUN ] MpiComm.SingleRankNoComm 19: [ OK ] MpiComm.SingleRankNoComm (0 ms) 19: [ RUN ] MpiComm.CommWorld 19: [ OK ] MpiComm.CommWorld (7 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (3 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (4 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (7 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (0 ms) 19: [ RUN ] MpiComm.ConstructorThrowsOnNull 19: [ OK ] MpiComm.ConstructorThrowsOnNull (0 ms) 19: [ RUN ] MpiComm.CopyConstructorWorks 19: [ OK ] MpiComm.CopyConstructorWorks (0 ms) 19: [ RUN ] MpiComm.AssigmentWorks 19: [ OK ] MpiComm.AssigmentWorks (0 ms) 19: [ RUN ] MpiComm.AssigmentWorksForSelf 19: [ OK ] MpiComm.AssigmentWorksForSelf (1 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorks 19: [ OK ] MpiComm.MoveAssigmentWorks (0 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 19: [ OK ] MpiComm.MoveAssigmentWorksForSelf (0 ms) 19: [----------] 12 tests from MpiComm (29 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 12 tests from 1 test suite ran. (29 ms total) 19: [ PASSED ] 12 tests. 19/103 Test #19: MpiCommTests .............................. Passed 0.05 sec test 20 Start 20: UtilityMpiUnitTests 20: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 20: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/utility/tests 20: Test timeout computed to be: 30 20: [==========] Running 7 tests from 2 test suites. 20: [----------] Global test environment set-up. 20: [----------] 5 tests from CoordinateExceptionHandlingTest 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow (0 ms) 20: [----------] 5 tests from CoordinateExceptionHandlingTest (1 ms total) 20: 20: [----------] 2 tests from PhysicalNodeCommunicatorTest 20: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 20: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 20: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 20: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 20: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 7 tests from 2 test suites ran. (2 ms total) 20: [ PASSED ] 7 tests. 20/103 Test #20: UtilityMpiUnitTests ....................... Passed 0.03 sec test 21 Start 21: AwhTest 21: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/AwhTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/awh/tests 21: Test timeout computed to be: 30 21: [==========] Running 27 tests from 10 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from SerializationTest 21: [ RUN ] SerializationTest.CanSerializeDimParams 21: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 21: [ RUN ] SerializationTest.CanSerializeBiasParams 21: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 21: [ RUN ] SerializationTest.CanSerializeAwhParams 21: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 21: [----------] 3 tests from SerializationTest (0 ms total) 21: 21: [----------] 1 test from BiasTest 21: [ RUN ] BiasTest.DetectsCovering 21: [ OK ] BiasTest.DetectsCovering (1 ms) 21: [----------] 1 test from BiasTest (1 ms total) 21: 21: [----------] 1 test from biasGridTest 21: [ RUN ] biasGridTest.neighborhood 21: [ OK ] biasGridTest.neighborhood (2 ms) 21: [----------] 1 test from biasGridTest (2 ms total) 21: 21: [----------] 2 tests from BiasSharingTest 21: [ RUN ] BiasSharingTest.SharingWorks 21: [ OK ] BiasSharingTest.SharingWorks (6 ms) 21: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 21: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (68 ms) 21: [----------] 2 tests from BiasSharingTest (75 ms total) 21: 21: [----------] 2 tests from BiasFepLambdaStateTest 21: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 21: [ OK ] BiasFepLambdaStateTest.DetectsCovering (7 ms) 21: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 21: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 21: [----------] 2 tests from BiasFepLambdaStateTest (8 ms total) 21: 21: [----------] 8 tests from WithParameters/BiasTest 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (1 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (1 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (1 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (1 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (1 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (1 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (1 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (1 ms) 21: [----------] 8 tests from WithParameters/BiasTest (10 ms total) 21: 21: [----------] 2 tests from WithParameters/BiasStateTest 21: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 21: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 21: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 21: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 21: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 21: 21: [----------] 1 test from WithParameters/UserInputTest 21: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 21: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 21: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 21: 21: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 21: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 21: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (15 ms) 21: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 21: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (15 ms) 21: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 21: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (15 ms) 21: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 21: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (15 ms) 21: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (63 ms total) 21: 21: [----------] 3 tests from WithParameters/FrictionMetricTest 21: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 21: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 21: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 21: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (2 ms) 21: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 21: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (43 ms) 21: [----------] 3 tests from WithParameters/FrictionMetricTest (53 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 27 tests from 10 test suites ran. (217 ms total) 21: [ PASSED ] 27 tests. 21/103 Test #21: AwhTest ................................... Passed 0.25 sec test 22 Start 22: DensityFittingAppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/densityfitting/tests 22: Test timeout computed to be: 30 22: [==========] Running 18 tests from 4 test suites. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from DensityFittingTest 22: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 22: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 22: [ RUN ] DensityFittingTest.SingleAtom 22: [ OK ] DensityFittingTest.SingleAtom (0 ms) 22: [----------] 2 tests from DensityFittingTest (1 ms total) 22: 22: [----------] 7 tests from DensityFittingAmplitudeLookupTest 22: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 22: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 22: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 22: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 22: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 22: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 22: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 22: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 22: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 22: 22: [----------] 1 test from DensityFittingForceProviderState 22: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 22: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 22: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 22: 22: [----------] 8 tests from DensityFittingOptionsTest 22: [ RUN ] DensityFittingOptionsTest.DefaultParameters 22: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 22: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 22: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 22: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 22: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 22: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 22: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 22: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 22: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 22: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 22: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 22: [ RUN ] DensityFittingOptionsTest.KvtToInternal 22: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 22: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 22: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 22: [----------] 8 tests from DensityFittingOptionsTest (1 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 18 tests from 4 test suites ran. (3 ms total) 22: [ PASSED ] 18 tests. 22/103 Test #22: DensityFittingAppliedForcesUnitTest ....... Passed 0.03 sec test 23 Start 23: QMMMAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests 23: Test timeout computed to be: 30 23: [==========] Running 28 tests from 7 test suites. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from QMMMInputGeneratorTest 23: [ RUN ] QMMMInputGeneratorTest.CanConstruct 23: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 23: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 23: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 23: [----------] 2 tests from QMMMInputGeneratorTest (0 ms total) 23: 23: [----------] 6 tests from QMMMTopologyPreprocessorTest 23: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: Setting the LD random seed to -26611781 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (12 ms) 23: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: Setting the LD random seed to 520043903 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (10 ms) 23: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: 23: WARNING 1 [file unknown]: 23: Total charge of your embedded system differs from classical system! 23: Consider manually spreading -0.41000 charge over MM atoms near to the 23: embedded region 23: 23: 23: Setting the LD random seed to -1074004487 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (9 ms) 23: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 63.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 129.093 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: 23: WARNING 1 [file unknown]: 23: Total charge of your embedded system differs from classical system! 23: Consider manually spreading 0.11440 charge over MM atoms near to the 23: embedded region 23: 23: 23: Setting the LD random seed to -537460739 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (26 ms) 23: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: 23: NOTE 2 [file unknown]: 23: You are using constraints on all bonds, whereas the forcefield has been 23: parametrized only with constraints involving hydrogen atoms. We suggest 23: using constraints = h-bonds instead, this will also improve performance. 23: 23: 23: NOTE 3 [file unknown]: 23: For energy conservation with LINCS, lincs_iter should be 2 or larger. 23: 23: 23: Number of degrees of freedom in T-Coupling group rest is 42.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 193.640 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 5 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: 23: WARNING 1 [file unknown]: 23: Total charge of your embedded system differs from classical system! 23: Consider manually spreading 0.11440 charge over MM atoms near to the 23: embedded region 23: 23: 23: 23: WARNING 2 [file unknown]: 23: Your embedded subsystem has a lot of constrained bonds. They probably 23: have been generated automatically. That could produce artifacts in the 23: simulation. Consider constraints = none in the mdp file. 23: 23: 23: Setting the LD random seed to -343998482 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: turning all bonds into constraints... 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (26 ms) 23: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Number of degrees of freedom in T-Coupling group rest is 45.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 23: Setting the LD random seed to -99815506 23: 23: Generated 3 of the 6 non-bonded parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'VSTEST' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 23: 23: Cleaning up constraints and constant bonded interactions with virtual sites 23: Analysing residue names: 23: There are: 1 Other residues 23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (12 ms) 23: [----------] 6 tests from QMMMTopologyPreprocessorTest (97 ms total) 23: 23: [----------] 9 tests from QMMMOptionsTest 23: [ RUN ] QMMMOptionsTest.DefaultParameters 23: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] QMMMOptionsTest.OptionSetsActive 23: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 23: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 23: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 23: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 23: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 23: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 23: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 23: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 23: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 23: [ OK ] QMMMOptionsTest.CP2KInputProcessing (1 ms) 23: [----------] 9 tests from QMMMOptionsTest (3 ms total) 23: 23: [----------] 3 tests from QMMMForceProviderStateTest 23: [ RUN ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint 23: [ OK ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint (0 ms) 23: [ RUN ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent 23: [ OK ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent (0 ms) 23: [ RUN ] QMMMForceProviderStateTest.MissingStateWhenNoData 23: [ OK ] QMMMForceProviderStateTest.MissingStateWhenNoData (0 ms) 23: [----------] 3 tests from QMMMForceProviderStateTest (0 ms total) 23: 23: [----------] 1 test from QMMMForceProviderTest 23: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 23: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 23: [----------] 1 test from QMMMForceProviderTest (0 ms total) 23: 23: [----------] 1 test from QMMMTest 23: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 23: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 23: [----------] 1 test from QMMMTest (0 ms total) 23: 23: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink (0 ms) 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink (0 ms) 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink (0 ms) 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink (0 ms) 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink (0 ms) 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink (0 ms) 23: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest (2 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 28 tests from 7 test suites ran. (105 ms total) 23: [ PASSED ] 28 tests. 23/103 Test #23: QMMMAppliedForcesUnitTest ................. Passed 0.13 sec test 24 Start 24: ColvarsAppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests 24: Test timeout computed to be: 30 24: [==========] Running 16 tests from 4 test suites. 24: [----------] Global test environment set-up. 24: [----------] 1 test from ColvarsTest 24: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 24: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 24: [----------] 1 test from ColvarsTest (0 ms total) 24: 24: [----------] 6 tests from ColvarsOptionsTest 24: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 24: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 24: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 24: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 24: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 24: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 24: [ RUN ] ColvarsOptionsTest.OptionSetsActive 24: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 24: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Setting the LD random seed to -80817157 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (17 ms) 24: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 24: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 24: [----------] 6 tests from ColvarsOptionsTest (19 ms total) 24: 24: [----------] 4 tests from ColvarsPreProcessorTest 24: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Setting the LD random seed to 1856732159 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (9 ms) 24: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Setting the LD random seed to 2144852979 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (12 ms) 24: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Setting the LD random seed to -545851617 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (13 ms) 24: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Setting the LD random seed to -327689 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (11 ms) 24: [----------] 4 tests from ColvarsPreProcessorTest (47 ms total) 24: 24: [----------] 5 tests from ColvarsForceProviderTest 24: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 24: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (1 ms) 24: [ RUN ] ColvarsForceProviderTest.SimpleInputs 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Setting the LD random seed to 2128082935 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsForceProviderTest.SimpleInputs (11 ms) 24: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Setting the LD random seed to 1945873781 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (10 ms) 24: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Setting the LD random seed to 989589295 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsForceProviderTest.CalculateForces4water (12 ms) 24: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 66.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 24: NVE simulation: will use the initial temperature of 300.368 K for 24: determining the Verlet buffer size 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 24: Setting the LD random seed to 1911336305 24: 24: Generated 2211 of the 2211 non-bonded parameter combinations 24: 24: Generated 2211 of the 2211 1-4 parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 24: Analysing residue names: 24: There are: 2 Protein residues 24: Analysing Protein... 24: 24: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 24: 24: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 24: 24: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 24: 24: Note that mdrun will redetermine rlist based on the actual pair-list setup 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (32 ms) 24: [----------] 5 tests from ColvarsForceProviderTest (68 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 16 tests from 4 test suites ran. (136 ms total) 24: [ PASSED ] 16 tests. 24/103 Test #24: ColvarsAppliedForcesUnitTest .............. Passed 0.16 sec test 25 Start 25: PlumedAppliedForcesUnitTests 25: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests 25: Test timeout computed to be: 30 25: [==========] Running 8 tests from 1 test suite. 25: [----------] Global test environment set-up. 25: [----------] 8 tests from PlumedOptionsTest 25: [ RUN ] PlumedOptionsTest.defaultConstructor 25: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) 25: [ RUN ] PlumedOptionsTest.setTimeStep 25: [ OK ] PlumedOptionsTest.setTimeStep (1 ms) 25: [ RUN ] PlumedOptionsTest.setStartingBehavior 25: [ OK ] PlumedOptionsTest.setStartingBehavior (0 ms) 25: [ RUN ] PlumedOptionsTest.setPlumedFile 25: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 25: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 25: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 25: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 25: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 25: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 25: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 25: [ RUN ] PlumedOptionsTest.setTopology 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: 25: NOTE 2 [file angles1.top, line 72]: 25: In moleculetype 'butane' 4 atoms are not bound by a potential or 25: constraint to any other atom in the same moleculetype. Although 25: technically this might not cause issues in a simulation, this often means 25: that the user forgot to add a bond/potential/constraint or put multiple 25: molecules in the same moleculetype definition by mistake. Run with -v to 25: get information for each atom. 25: 25: Number of degrees of freedom in T-Coupling group rest is 9.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 25: NVE simulation: will use the initial temperature of 238.919 K for 25: determining the Verlet buffer size 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Number of degrees of freedom in T-Coupling group rest is 17493.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 25: NVE simulation: will use the initial temperature of 67.983 K for 25: determining the Verlet buffer size 25: 25: 25: There were 2 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Number of degrees of freedom in T-Coupling group rest is 9.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: There were 2 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Number of degrees of freedom in T-Coupling group rest is 9.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 18.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 25: NVE simulation: will use the initial temperature of 135.187 K for 25: determining the Verlet buffer size 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 25: Setting the LD random seed to -805581834 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: Setting the LD random seed to -27303938 25: 25: Generated 3 of the 3 non-bonded parameter combinations 25: 25: Excluding 3 bonded neighbours molecule type 'butane' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/angles1.gro' 25: Analysing residue names: 25: There are: 1 Other residues 25: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: Setting the LD random seed to -639810961 25: 25: Generated 1 of the 1 non-bonded parameter combinations 25: 25: Excluding 1 bonded neighbours molecule type 'Argon' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon5832.gro' 25: Analysing residue names: 25: There are: 5832 Other residues 25: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: Setting the LD random seed to 2087934623 25: 25: Generated 1 of the 1 non-bonded parameter combinations 25: 25: Excluding 1 bonded neighbours molecule type 'ArgonA' 25: 25: Excluding 1 bonded neighbours molecule type 'ArgonB' 25: 25: Excluding 1 bonded neighbours molecule type 'ArgonC' 25: 25: Excluding 1 bonded neighbours molecule type 'ArgonD' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Other residues 25: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 25: 25: This run will generate roughly 0 Mb of data 25: Setting the LD random seed to -1376257153 25: 25: Generated 1 of the 1 non-bonded parameter combinations 25: 25: Excluding 1 bonded neighbours molecule type 'Dipole' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 25: Analysing residue names: 25: There are: 2 Other residues 25: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 25: 25: This run will generate roughly 0 Mb of data 25: Setting the LD random seed to 1249901151 25: 25: Generated 331705 of the 331705 non-bonded parameter combinations 25: 25: Generated 331705 of the 331705 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Excluding 3 bonded neighbours molecule type 'methane' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 25: Analysing residue names: 25: There are: 1 Water residues 25: There are: 1 Other residues 25: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] PlumedOptionsTest.setTopology (900 ms) 25: [----------] 8 tests from PlumedOptionsTest (903 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 8 tests from 1 test suite ran. (903 ms total) 25: [ PASSED ] 8 tests. 25/103 Test #25: PlumedAppliedForcesUnitTests .............. Passed 0.94 sec test 26 Start 26: PlumedMDTests 26: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/PlumedMDTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/plumed/tests 26: Test timeout computed to be: 600 26: [==========] Running 2 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 2 tests from SimplePlumedMD/PlumedRun 26: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 26: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 26: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 26: 26: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 26: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 26: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 26: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 26: 26: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 26: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 2 tests from 1 test suite ran. (16 ms total) 26: [ PASSED ] 0 tests. 26: [ SKIPPED ] 2 tests, listed below: 26: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 26: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 26/103 Test #26: PlumedMDTests ............................. Passed 0.04 sec test 27 Start 27: NNPotAppliedForcesUnitTest 27: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 27: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests 27: Test timeout computed to be: 30 27: [==========] Running 17 tests from 4 test suites. 27: [----------] Global test environment set-up. 27: [----------] 1 test from NNPotTest 27: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 27: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 27: [----------] 1 test from NNPotTest (0 ms total) 27: 27: [----------] 5 tests from NNPotOptionsTest 27: [ RUN ] NNPotOptionsTest.DefaultParameters 27: [ OK ] NNPotOptionsTest.DefaultParameters (36 ms) 27: [ RUN ] NNPotOptionsTest.OptionSetsActive 27: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 27: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 27: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 27: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 27: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 27: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 27: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 27: [----------] 5 tests from NNPotOptionsTest (37 ms total) 27: 27: [----------] 1 test from NNPotForceProviderTest 27: [ RUN ] NNPotForceProviderTest.CanConstruct 27: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 27: [----------] 1 test from NNPotForceProviderTest (0 ms total) 27: 27: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 21.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Setting the LD random seed to -30949409 27: 27: Generated 10 of the 10 non-bonded parameter combinations 27: 27: Generated 10 of the 10 1-4 parameter combinations 27: 27: Excluding 2 bonded neighbours molecule type 'SOL' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 27: Analysing residue names: 27: There are: 4 Water residues 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 (11 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 21.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Setting the LD random seed to -1212164353 27: 27: Generated 10 of the 10 non-bonded parameter combinations 27: 27: Generated 10 of the 10 1-4 parameter combinations 27: 27: Excluding 2 bonded neighbours molecule type 'SOL' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 27: Analysing residue names: 27: There are: 4 Water residues 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 (10 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 21.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Setting the LD random seed to -1092691081 27: 27: Generated 10 of the 10 non-bonded parameter combinations 27: 27: Generated 10 of the 10 1-4 parameter combinations 27: 27: Excluding 2 bonded neighbours molecule type 'SOL' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 27: Analysing residue names: 27: There are: 4 Water residues 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 (9 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 21.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Setting the LD random seed to -1090650166 27: 27: Generated 10 of the 10 non-bonded parameter combinations 27: 27: Generated 10 of the 10 1-4 parameter combinations 27: 27: Excluding 2 bonded neighbours molecule type 'SOL' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 27: Analysing residue names: 27: There are: 4 Water residues 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 (10 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 63.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 27: NVE simulation: will use the initial temperature of 129.093 K for 27: determining the Verlet buffer size 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Setting the LD random seed to 2078064603 27: 27: Generated 2145 of the 2145 non-bonded parameter combinations 27: 27: Generated 2145 of the 2145 1-4 parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 27: Analysing residue names: 27: There are: 3 Protein residues 27: Analysing Protein... 27: 27: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 27: 27: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 27: 27: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 27: 27: Note that mdrun will redetermine rlist based on the actual pair-list setup 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 (24 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 63.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 27: NVE simulation: will use the initial temperature of 129.093 K for 27: determining the Verlet buffer size 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: 27: WARNING 1 [file unknown]: 27: Total charge of your embedded system differs from classical system! 27: Consider manually spreading 0.11440 charge over MM atoms near to the 27: embedded region 27: 27: 27: Setting the LD random seed to -303076360 27: 27: Generated 2145 of the 2145 non-bonded parameter combinations 27: 27: Generated 2145 of the 2145 1-4 parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 27: Analysing residue names: 27: There are: 3 Protein residues 27: Analysing Protein... 27: 27: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 27: 27: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 27: 27: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 27: 27: Note that mdrun will redetermine rlist based on the actual pair-list setup 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 (24 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: 27: NOTE 2 [file unknown]: 27: You are using constraints on all bonds, whereas the forcefield has been 27: parametrized only with constraints involving hydrogen atoms. We suggest 27: using constraints = h-bonds instead, this will also improve performance. 27: 27: 27: NOTE 3 [file unknown]: 27: For energy conservation with LINCS, lincs_iter should be 2 or larger. 27: 27: 27: Number of degrees of freedom in T-Coupling group rest is 42.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 27: NVE simulation: will use the initial temperature of 193.640 K for 27: determining the Verlet buffer size 27: 27: 27: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 5 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: 27: WARNING 1 [file unknown]: 27: Your embedded subsystem has a lot of constrained bonds. They probably 27: have been generated automatically. That could produce artifacts in the 27: simulation. Consider constraints = none in the mdp file. 27: 27: 27: Setting the LD random seed to -1446913 27: 27: Generated 2145 of the 2145 non-bonded parameter combinations 27: 27: Generated 2145 of the 2145 1-4 parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 27: 27: turning all bonds into constraints... 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 27: Analysing residue names: 27: There are: 3 Protein residues 27: Analysing Protein... 27: 27: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 27: 27: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 27: 27: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 27: 27: Note that mdrun will redetermine rlist based on the actual pair-list setup 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 (26 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: 27: NOTE 2 [file unknown]: 27: You are using constraints on all bonds, whereas the forcefield has been 27: parametrized only with constraints involving hydrogen atoms. We suggest 27: using constraints = h-bonds instead, this will also improve performance. 27: 27: 27: NOTE 3 [file unknown]: 27: For energy conservation with LINCS, lincs_iter should be 2 or larger. 27: 27: 27: Number of degrees of freedom in T-Coupling group rest is 42.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 27: NVE simulation: will use the initial temperature of 193.640 K for 27: determining the Verlet buffer size 27: 27: 27: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 5 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: 27: WARNING 1 [file unknown]: 27: Total charge of your embedded system differs from classical system! 27: Consider manually spreading 0.11440 charge over MM atoms near to the 27: embedded region 27: 27: 27: 27: WARNING 2 [file unknown]: 27: Your embedded subsystem has a lot of constrained bonds. They probably 27: have been generated automatically. That could produce artifacts in the 27: simulation. Consider constraints = none in the mdp file. 27: 27: 27: Setting the LD random seed to -1358989828 27: 27: Generated 2145 of the 2145 non-bonded parameter combinations 27: 27: Generated 2145 of the 2145 1-4 parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 27: 27: turning all bonds into constraints... 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 27: Analysing residue names: 27: There are: 3 Protein residues 27: Analysing Protein... 27: 27: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 27: 27: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 27: 27: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 27: 27: Note that mdrun will redetermine rlist based on the actual pair-list setup 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 (26 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Number of degrees of freedom in T-Coupling group rest is 45.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Setting the LD random seed to 1979183063 27: 27: Generated 3 of the 6 non-bonded parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'VSTEST' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 27: 27: Cleaning up constraints and constant bonded interactions with virtual sites 27: Analysing residue names: 27: There are: 1 Other residues 27: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 (10 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Number of degrees of freedom in T-Coupling group rest is 45.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 27: Setting the LD random seed to 2145347555 27: 27: Generated 3 of the 6 non-bonded parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'VSTEST' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 27: 27: Cleaning up constraints and constant bonded interactions with virtual sites 27: Analysing residue names: 27: There are: 1 Other residues 27: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 (11 ms) 27: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest (166 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 17 tests from 4 test suites ran. (205 ms total) 27: [ PASSED ] 17 tests. 27/103 Test #27: NNPotAppliedForcesUnitTest ................ Passed 0.25 sec test 28 Start 28: AppliedForcesUnitTest 28: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 28: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/applied_forces/tests 28: Test timeout computed to be: 30 28: [==========] Running 3 tests from 1 test suite. 28: [----------] Global test environment set-up. 28: [----------] 3 tests from ElectricFieldTest 28: [ RUN ] ElectricFieldTest.Static 28: [ OK ] ElectricFieldTest.Static (0 ms) 28: [ RUN ] ElectricFieldTest.Oscillating 28: [ OK ] ElectricFieldTest.Oscillating (0 ms) 28: [ RUN ] ElectricFieldTest.Pulsed 28: [ OK ] ElectricFieldTest.Pulsed (0 ms) 28: [----------] 3 tests from ElectricFieldTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 3 tests from 1 test suite ran. (0 ms total) 28: [ PASSED ] 3 tests. 28/103 Test #28: AppliedForcesUnitTest ..................... Passed 0.02 sec test 29 Start 29: ListedForcesTest 29: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/ListedForcesTest.xml" 29: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/listed_forces/tests 29: Test timeout computed to be: 30 29: [==========] Running 132 tests from 9 test suites. 29: [----------] Global test environment set-up. 29: [----------] 24 tests from Bond/ListedForcesTest 29: [ RUN ] Bond/ListedForcesTest.Ifunc/0 29: [ OK ] Bond/ListedForcesTest.Ifunc/0 (3 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/1 29: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/2 29: [ OK ] Bond/ListedForcesTest.Ifunc/2 (1 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/3 29: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/4 29: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/5 29: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/6 29: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/7 29: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/8 29: [ OK ] Bond/ListedForcesTest.Ifunc/8 (1 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/9 29: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/10 29: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/11 29: [ OK ] Bond/ListedForcesTest.Ifunc/11 (1 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/12 29: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/13 29: [ OK ] Bond/ListedForcesTest.Ifunc/13 (1 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/14 29: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/15 29: [ OK ] Bond/ListedForcesTest.Ifunc/15 (1 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/16 29: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/17 29: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/18 29: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/19 29: [ OK ] Bond/ListedForcesTest.Ifunc/19 (1 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/20 29: [ OK ] Bond/ListedForcesTest.Ifunc/20 (1 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/21 29: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/22 29: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/23 29: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 29: [----------] 24 tests from Bond/ListedForcesTest (24 ms total) 29: 29: [----------] 33 tests from Angle/ListedForcesTest 29: [ RUN ] Angle/ListedForcesTest.Ifunc/0 29: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/1 29: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/2 29: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/3 29: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/4 29: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/5 29: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/6 29: [ OK ] Angle/ListedForcesTest.Ifunc/6 (1 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/7 29: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/8 29: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/9 29: [ OK ] Angle/ListedForcesTest.Ifunc/9 (1 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/10 29: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/11 29: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/12 29: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/13 29: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/14 29: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/15 29: [ OK ] Angle/ListedForcesTest.Ifunc/15 (1 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/16 29: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/17 29: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/18 29: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/19 29: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/20 29: [ OK ] Angle/ListedForcesTest.Ifunc/20 (1 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/21 29: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/22 29: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/23 29: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/24 29: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/25 29: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/26 29: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/27 29: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/28 29: [ OK ] Angle/ListedForcesTest.Ifunc/28 (1 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/29 29: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/30 29: [ OK ] Angle/ListedForcesTest.Ifunc/30 (1 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/31 29: [ OK ] Angle/ListedForcesTest.Ifunc/31 (1 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/32 29: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 29: [----------] 33 tests from Angle/ListedForcesTest (24 ms total) 29: 29: [----------] 18 tests from Dihedral/ListedForcesTest 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (1 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (1 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (1 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (1 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 29: [----------] 18 tests from Dihedral/ListedForcesTest (13 ms total) 29: 29: [----------] 12 tests from Polarize/ListedForcesTest 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 29: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 29: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 29: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 29: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 29: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 29: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 29: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 29: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 29: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 29: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 29: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 29: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 29: [----------] 12 tests from Polarize/ListedForcesTest (5 ms total) 29: 29: [----------] 18 tests from Restraints/ListedForcesTest 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 29: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (1 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 29: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 29: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (1 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 29: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 29: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 29: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 29: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (1 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 29: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 29: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (1 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 29: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 29: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 29: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 29: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 29: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 29: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 29: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 29: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 29: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 29: [----------] 18 tests from Restraints/ListedForcesTest (14 ms total) 29: 29: [----------] 3 tests from BondZeroLength/ListedForcesTest 29: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 29: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 29: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 29: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 29: [----------] 3 tests from BondZeroLength/ListedForcesTest (1 ms total) 29: 29: [----------] 3 tests from AngleZero/ListedForcesTest 29: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 29: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (1 ms) 29: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 29: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (1 ms) 29: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 29: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 29: [----------] 3 tests from AngleZero/ListedForcesTest (3 ms total) 29: 29: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (2 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (1 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (2 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (1 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (1 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (1 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 29: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (13 ms total) 29: 29: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (1 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (1 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 29: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (7 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 132 tests from 9 test suites ran. (108 ms total) 29: [ PASSED ] 132 tests. 29/103 Test #29: ListedForcesTest .......................... Passed 0.15 sec test 30 Start 30: NbnxmTests 30: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nbnxm-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/NbnxmTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests 30: Test timeout computed to be: 30 30: [==========] Running 529 tests from 4 test suites. 30: [----------] Global test environment set-up. 30: [----------] 19 tests from KernelSetupTest 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 30: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 30: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 30: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 30: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 30: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 30: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeNone 30: [ OK ] KernelSetupTest.getCoulombKernelTypeNone (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 30: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 30: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 30: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 30: [----------] 19 tests from KernelSetupTest (0 ms total) 30: 30: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest 30: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 30: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 30: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 30: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 30: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 30: 30: [----------] 504 tests from Combinations/NbnxmKernelTest 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (10 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (8 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (9 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (8 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (9 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (9 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (9 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [----------] 504 tests from Combinations/NbnxmKernelTest (538 ms total) 30: 30: [----------] 4 tests from WithParameters/PlainPairlistTest 30: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 30: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 (1 ms) 30: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 30: ./src/gromacs/nbnxm/tests/plainpairlist.cpp:235: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 (0 ms) 30: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 30: ./src/gromacs/nbnxm/tests/plainpairlist.cpp:241: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 (0 ms) 30: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 30: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 (1 ms) 30: [----------] 4 tests from WithParameters/PlainPairlistTest (2 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 529 tests from 4 test suites ran. (542 ms total) 30: [ PASSED ] 95 tests. 30: [ SKIPPED ] 434 tests, listed below: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 30: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 30/103 Test #30: NbnxmTests ................................ Passed 0.61 sec test 31 Start 31: NbnxmGpuTests 31: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/NbnxmGpuTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests 31: Test timeout computed to be: 30 31: This test program does NOT link in any test case. Please make sure this is intended. 31: [==========] Running 0 tests from 0 test suites. 31: [==========] 0 tests from 0 test suites ran. (0 ms total) 31: [ PASSED ] 0 tests. 31/103 Test #31: NbnxmGpuTests ............................. Passed 0.04 sec test 32 Start 32: GmxlibTests 32: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/GmxlibTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests 32: Test timeout computed to be: 30 32: [==========] Running 78 tests from 2 test suites. 32: [----------] Global test environment set-up. 32: [----------] 72 tests from NBInteraction/NonbondedFepTest 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (1 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 32: [----------] 72 tests from NBInteraction/NonbondedFepTest (31 ms total) 32: 32: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 32: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (2 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 78 tests from 2 test suites ran. (33 ms total) 32: [ PASSED ] 78 tests. 32/103 Test #32: GmxlibTests ............................... Passed 0.08 sec test 33 Start 33: GmxlibGpuTests 33: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/nonbonded-fep-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/GmxlibGpuTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/nbnxm/tests 33: Test timeout computed to be: 30 33: This test program does NOT link in any test case. Please make sure this is intended. 33: [==========] Running 0 tests from 0 test suites. 33: [==========] 0 tests from 0 test suites ran. (0 ms total) 33: [ PASSED ] 0 tests. 33/103 Test #33: GmxlibGpuTests ............................ Passed 0.04 sec test 34 Start 34: CommandLineUnitTests 34: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests 34: Test timeout computed to be: 30 34: [==========] Running 60 tests from 7 test suites. 34: [----------] Global test environment set-up. 34: [----------] 3 tests from CommandLineHelpModuleTest 34: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 34: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 34: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 34: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 34: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 34: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 34: [----------] 3 tests from CommandLineHelpModuleTest (3 ms total) 34: 34: [----------] 7 tests from CommandLineHelpWriterTest 34: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 34: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 34: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 34: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 34: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 34: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 34: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 34: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 34: [----------] 7 tests from CommandLineHelpWriterTest (3 ms total) 34: 34: [----------] 6 tests from CommandLineModuleManagerTest 34: [ RUN ] CommandLineModuleManagerTest.RunsModule 34: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 34: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 34: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 34: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 34: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 34: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 34: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 34: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 34: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 34: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 34: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 34: [----------] 6 tests from CommandLineModuleManagerTest (1 ms total) 34: 34: [----------] 13 tests from CommandLineParserTest 34: [ RUN ] CommandLineParserTest.HandlesSingleValues 34: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 34: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 34: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 34: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 34: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 34: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesString 34: [ OK ] CommandLineParserTest.HandlesString (0 ms) 34: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 34: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 34: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 34: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 34: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 34: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 34: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 34: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 34: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 34: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 34: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 34: [----------] 13 tests from CommandLineParserTest (1 ms total) 34: 34: [----------] 6 tests from CommandLineProgramContextTest 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 34: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 34: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 34: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 34: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 34: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 34: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 34: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 34: 34: [----------] 3 tests from OutputNamesTest 34: [ RUN ] OutputNamesTest.CanBeSuffixed 34: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 34: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 34: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 34: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 34: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 34: [----------] 3 tests from OutputNamesTest (0 ms total) 34: 34: [----------] 22 tests from ParseCommonArgsTest 34: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 34: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 34: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 34: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 34: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 34: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 34: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 34: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 34: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 34: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 34: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 34: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 34: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 34: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 34: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 34: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 34: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 34: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 34: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 34: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 34: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 34: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 34: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 34: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 34: Value is /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 34: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 34: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 34: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 34: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 34: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (9 ms) 34: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 34: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 34: [----------] 22 tests from ParseCommonArgsTest (12 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 60 tests from 7 test suites ran. (23 ms total) 34: [ PASSED ] 60 tests. 34/103 Test #34: CommandLineUnitTests ...................... Passed 0.05 sec test 35 Start 35: DomDecTests 35: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/DomDecTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests 35: Test timeout computed to be: 30 35: [==========] Running 9 tests from 2 test suites. 35: [----------] Global test environment set-up. 35: [----------] 7 tests from HashedMap 35: [ RUN ] HashedMap.InsertsFinds 35: [ OK ] HashedMap.InsertsFinds (0 ms) 35: [ RUN ] HashedMap.NegativeKeysWork 35: [ OK ] HashedMap.NegativeKeysWork (0 ms) 35: [ RUN ] HashedMap.InsertsErases 35: [ OK ] HashedMap.InsertsErases (0 ms) 35: [ RUN ] HashedMap.InsertsOrAssigns 35: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 35: [ RUN ] HashedMap.Clears 35: [ OK ] HashedMap.Clears (0 ms) 35: [ RUN ] HashedMap.LinkedEntries 35: [ OK ] HashedMap.LinkedEntries (0 ms) 35: [ RUN ] HashedMap.ResizesTable 35: [ OK ] HashedMap.ResizesTable (0 ms) 35: [----------] 7 tests from HashedMap (0 ms total) 35: 35: [----------] 2 tests from LocalAtomSetManager 35: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 35: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 35: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 35: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 35: [----------] 2 tests from LocalAtomSetManager (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 9 tests from 2 test suites ran. (0 ms total) 35: [ PASSED ] 9 tests. 35/103 Test #35: DomDecTests ............................... Passed 0.02 sec test 36 Start 36: DomDecMpiTests 36: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/DomDecMpiTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/domdec/tests 36: Test timeout computed to be: 30 36: [==========] Running 8 tests from 1 test suite. 36: [----------] Global test environment set-up. 36: [----------] 8 tests from Works/HaloExchangeTest 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/0 36: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/0 (1 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/1 36: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/1 (2 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/2 36: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/2 (7 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/3 36: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/3 (11 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/0 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 36: 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 (0 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/1 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 36: 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 (0 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/2 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 36: 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 (0 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/3 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 36: 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 (0 ms) 36: [----------] 8 tests from Works/HaloExchangeTest (26 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 8 tests from 1 test suite ran. (27 ms total) 36: [ PASSED ] 4 tests. 36: [ SKIPPED ] 4 tests, listed below: 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 36/103 Test #36: DomDecMpiTests ............................ Passed 0.07 sec test 37 Start 37: EwaldUnitTests 37: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/EwaldUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/ewald/tests 37: Test timeout computed to be: 30 37: [==========] Running 407 tests from 9 test suites. 37: [----------] Global test environment set-up. 37: [----------] 6 tests from SeparatePmeRanksPermittedTest 37: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 37: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 37: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 37: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 37: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 37: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 37: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 37: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 37: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 37: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 37: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 37: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 37: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 37: 37: [----------] 108 tests from Pme_SplineAndSpreadTest 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (8 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (56 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (9 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (64 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (6 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (28 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (18 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (51 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (21 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (30 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (95 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (20 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (62 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (95 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (24 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (62 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (94 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (6 ms) 37: [----------] 108 tests from Pme_SplineAndSpreadTest (957 ms total) 37: 37: [----------] 64 tests from Pme_SolveTest 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (14 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (29 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (23 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [----------] 64 tests from Pme_SolveTest (100 ms total) 37: 37: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (16 ms total) 37: 37: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (2 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 37: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (19 ms total) 37: 37: [----------] 64 tests from PmeDiffEps_SolveTest 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [----------] 64 tests from PmeDiffEps_SolveTest (33 ms total) 37: 37: [----------] 72 tests from Pme_GatherTest 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (2 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (2 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (2 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [----------] 72 tests from Pme_GatherTest (68 ms total) 37: 37: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 37: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 37: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 37: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 37: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 37: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 37: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 37: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 37: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (2 ms) 37: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 37: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 37: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (3 ms total) 37: 37: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (5 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 37: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (53 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 407 tests from 9 test suites ran. (1255 ms total) 37: [ PASSED ] 311 tests. 37: [ SKIPPED ] 96 tests, listed below: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37/103 Test #37: EwaldUnitTests ............................ Passed 1.32 sec test 38 Start 38: FFTUnitTests 38: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/FFTUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fft/tests 38: Test timeout computed to be: 1920 38: [==========] Running 15 tests from 4 test suites. 38: [----------] Global test environment set-up. 38: [----------] 2 tests from ManyFFTTest 38: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 38: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (7 ms) 38: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 38: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (26 ms) 38: [----------] 2 tests from ManyFFTTest (34 ms total) 38: 38: [----------] 1 test from FFTTest 38: [ RUN ] FFTTest.Real2DLength18_15Test 38: [ OK ] FFTTest.Real2DLength18_15Test (3 ms) 38: [----------] 1 test from FFTTest (4 ms total) 38: 38: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 38: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 38: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 38: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 38: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 38: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 38: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 38: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 38: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 38: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (7 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 38: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (9 ms) 38: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (29 ms total) 38: 38: [----------] 2 tests from Works/ParameterizedFFTTest3D 38: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 38: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (2 ms) 38: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 38: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (3 ms) 38: [----------] 2 tests from Works/ParameterizedFFTTest3D (6 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 15 tests from 4 test suites ran. (74 ms total) 38: [ PASSED ] 15 tests. 38/103 Test #38: FFTUnitTests .............................. Passed 0.12 sec test 39 Start 39: FmmInterfaceUnitTests 39: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/fmm-interface-tests "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/FmmInterfaceUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fmm/tests 39: Test timeout computed to be: 30 39: [==========] Running 18 tests from 4 test suites. 39: [----------] Global test environment set-up. 39: [----------] 10 tests from FmmMdpOptionsTest 39: [ RUN ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive 39: [ OK ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive 39: [ OK ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive 39: [ OK ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive 39: [ OK ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues 39: [ OK ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues (0 ms) 39: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder 39: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder (0 ms) 39: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder 39: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder (0 ms) 39: [ RUN ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive 39: [ OK ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive (1 ms) 39: [ RUN ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive 39: [ OK ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive 39: [ OK ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive (0 ms) 39: [----------] 10 tests from FmmMdpOptionsTest (4 ms total) 39: 39: [----------] 4 tests from FmmMdpValidatorTest 39: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings 39: 39: ERROR 1 [file unknown]: 39: ExaFMM expansion order must be greater than 0. 39: 39: 39: ERROR 1 [file unknown]: 39: ExaFMM direct range must be 2 when using GROMACS as a direct provider. 39: 39: 39: ERROR 1 [file unknown]: 39: Adaptive tree cannot be used for FMM when GROMACS is the direct provider. 39: Use a uniform tree instead. 39: 39: 39: ERROR 1 [file unknown]: 39: Maximum particles per cell for FMM must be set to a positive value when 39: using an adaptive tree. 39: 39: 39: ERROR 1 [file unknown]: 39: Tree depth for FMM is determined based on the domain decomposition grid 39: when using GROMACS as the direct provider and should not be set by the 39: user. 39: 39: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings (0 ms) 39: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings 39: 39: ERROR 1 [file unknown]: 39: FMSolvr tree depth must be greater than or equal to 0. 39: 39: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings (0 ms) 39: [ RUN ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings 39: [ OK ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings (0 ms) 39: [ RUN ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm 39: 39: ERROR 1 [file unknown]: 39: FMM requires Coulomb interaction type to be FMM, but got PME 39: 39: [ OK ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm (0 ms) 39: [----------] 4 tests from FmmMdpValidatorTest (1 ms total) 39: 39: [----------] 1 test from FmmForceProviderTest 39: [ RUN ] FmmForceProviderTest.ThrowsWhenConstructingStub 39: [ OK ] FmmForceProviderTest.ThrowsWhenConstructingStub (0 ms) 39: [----------] 1 test from FmmForceProviderTest (0 ms total) 39: 39: [----------] 3 tests from FmmForceProviderBuilderTest 39: [ RUN ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady 39: [ OK ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady (0 ms) 39: [ RUN ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup 39: [ OK ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup (0 ms) 39: [ RUN ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider 39: [ OK ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider (0 ms) 39: [----------] 3 tests from FmmForceProviderBuilderTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 18 tests from 4 test suites ran. (6 ms total) 39: [ PASSED ] 18 tests. 39/103 Test #39: FmmInterfaceUnitTests ..................... Passed 0.03 sec test 40 Start 40: GpuUtilsUnitTests 40: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests 40: Test timeout computed to be: 30 40: [==========] Running 67 tests from 22 test suites. 40: [----------] Global test environment set-up. 40: [----------] 2 tests from ClfftInitializer 40: [ RUN ] ClfftInitializer.SingleInitializationWorks 40: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 40: [ RUN ] ClfftInitializer.TwoInitializationsWork 40: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 40: [----------] 2 tests from ClfftInitializer (0 ms total) 40: 40: [----------] 1 test from DevicesAvailable 40: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 40: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 40: [----------] 1 test from DevicesAvailable (0 ms total) 40: 40: [----------] 1 test from DeviceStreamManagerTest 40: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 40: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 40: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 40: 40: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 40: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 40: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 40: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 40: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 40: 40: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 40: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 40: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 40: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 40: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 40: 40: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 40: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 40: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 40: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 40: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 40: 40: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 40: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 40: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 40: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 40: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 40: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 40: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 40: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 40: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 40: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 40: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 40: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 40: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 40: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 40: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 40: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 40: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 40: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 40: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 40: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 40: 40: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 40: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 40: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 40: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 40: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/0.Swap 40: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/0.Comparison 40: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 40: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 40: 40: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 40: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 40: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 40: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 40: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/1.Swap 40: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/1.Comparison 40: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 40: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 40: 40: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 40: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 40: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 40: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 40: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/2.Swap 40: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/2.Comparison 40: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 40: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 40: 40: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 40: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 40: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 40: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 40: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/3.Swap 40: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/3.Comparison 40: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 40: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 40: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 40: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 40: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 40: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 40: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 40: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 40: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 40: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 40: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 40: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 40: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 40: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 40: 40: [----------] 1 test from HostAllocatorUntypedTest 40: [ RUN ] HostAllocatorUntypedTest.Comparison 40: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 40: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 40: 40: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 40: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 40: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 40: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 40: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/0.Move 40: [ OK ] AllocatorTest/0.Move (0 ms) 40: [----------] 4 tests from AllocatorTest/0 (0 ms total) 40: 40: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 40: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 40: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 40: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 40: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/1.Move 40: [ OK ] AllocatorTest/1.Move (0 ms) 40: [----------] 4 tests from AllocatorTest/1 (0 ms total) 40: 40: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator,gmx::HostAllocationPolicy> 40: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 40: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 40: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 40: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/2.Move 40: [ OK ] AllocatorTest/2.Move (0 ms) 40: [----------] 4 tests from AllocatorTest/2 (0 ms total) 40: 40: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 40: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 40: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 40: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 40: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/3.Move 40: [ OK ] AllocatorTest/3.Move (0 ms) 40: [----------] 4 tests from AllocatorTest/3 (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 67 tests from 22 test suites ran. (1 ms total) 40: [ PASSED ] 67 tests. 40/103 Test #40: GpuUtilsUnitTests ......................... Passed 0.05 sec test 41 Start 41: GpuUtilsMpiTests 41: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/gpu_utils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/GpuUtilsMpiTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gpu_utils/tests 41: Test timeout computed to be: 30 41: [==========] Running 15 tests from 1 test suite. 41: [----------] Global test environment set-up. 41: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message (0 ms) 41: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/0_values_in_message 41: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/1_values_in_message 41: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/12000_values_in_message 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message (0 ms) 41: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest (5 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 15 tests from 1 test suite ran. (5 ms total) 41: [ PASSED ] 0 tests. 41: [ SKIPPED ] 15 tests, listed below: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 41: 41: YOU HAVE 3 DISABLED TESTS 41: 41/103 Test #41: GpuUtilsMpiTests .......................... Passed 0.05 sec test 42 Start 42: HardwareUnitTests 42: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/HardwareUnitTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/hardware/tests 42: Test timeout computed to be: 30 42: [==========] Running 22 tests from 10 test suites. 42: [----------] Global test environment set-up. 42: [----------] 1 test from CpuInfoTest 42: [ RUN ] CpuInfoTest.SupportLevel 42: [ OK ] CpuInfoTest.SupportLevel (0 ms) 42: [----------] 1 test from CpuInfoTest (0 ms total) 42: 42: [----------] 4 tests from HardwareTopologyTest 42: [ RUN ] HardwareTopologyTest.Execute 42: [ OK ] HardwareTopologyTest.Execute (15 ms) 42: [ RUN ] HardwareTopologyTest.HwlocExecute 42: [ OK ] HardwareTopologyTest.HwlocExecute (14 ms) 42: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 42: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (14 ms) 42: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 42: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (14 ms) 42: [----------] 4 tests from HardwareTopologyTest (58 ms total) 42: 42: [----------] 1 test from DevicesManagerTest 42: [ RUN ] DevicesManagerTest.Serialization 42: [ OK ] DevicesManagerTest.Serialization (0 ms) 42: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 42: [----------] 1 test from DevicesManagerTest (0 ms total) 42: 42: [----------] 1 test from UuidStringTest 42: [ RUN ] UuidStringTest.Works 42: [ OK ] UuidStringTest.Works (0 ms) 42: [----------] 1 test from UuidStringTest (0 ms total) 42: 42: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 42: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 42: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (58 ms) 42: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 42: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 42: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 42: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (1 ms) 42: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 42: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (1 ms) 42: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 42: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (1 ms) 42: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (64 ms total) 42: 42: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 42: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 42: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (4 ms) 42: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 42: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 42: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 42: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (1 ms) 42: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 42: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (1 ms) 42: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 42: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (1 ms) 42: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (10 ms total) 42: 42: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 42: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 42: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (2 ms) 42: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 42: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (2 ms) 42: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (5 ms total) 42: 42: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 42: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 42: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (11 ms) 42: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (11 ms total) 42: 42: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 42: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 42: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (15 ms) 42: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (15 ms total) 42: 42: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 42: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 42: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (22 ms) 42: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (22 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 22 tests from 10 test suites ran. (189 ms total) 42: [ PASSED ] 22 tests. 42: 42: YOU HAVE 1 DISABLED TEST 42: 42/103 Test #42: HardwareUnitTests ......................... Passed 0.22 sec test 43 Start 43: MathUnitTests 43: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MathUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/math/tests 43: Test timeout computed to be: 30 43: [==========] Running 293 tests from 40 test suites. 43: [----------] Global test environment set-up. 43: [----------] 1 test from EmptyArrayRefWithPaddingTest 43: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 43: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 43: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 43: 43: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 43: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 43: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 43: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 43: 43: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 43: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 43: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 43: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 43: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 43: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 43: 43: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 43: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 43: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 43: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 43: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 43: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 43: 43: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 43: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 43: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 43: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 43: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 43: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 43: 43: [----------] 2 tests from InvertBoxMatrixTest 43: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 43: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 43: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 43: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 43: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 43: 43: [----------] 8 tests from ComplexNumberTest 43: [ RUN ] ComplexNumberTest.RealComplexMultiply 43: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 43: [ RUN ] ComplexNumberTest.RealComplexExp 43: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexAdd 43: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexSubtract 43: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexMultiply 43: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexDivision 43: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexConjugate 43: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexAbs2 43: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 43: [----------] 8 tests from ComplexNumberTest (3 ms total) 43: 43: [----------] 11 tests from TranslateAndScaleTest 43: [ RUN ] TranslateAndScaleTest.identityTransformation 43: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 43: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 43: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 43: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 43: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 43: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 43: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 43: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingIdentity 43: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 43: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 43: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 43: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 43: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 43: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 43: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 43: 43: [----------] 3 tests from AffineTransformationTest 43: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 43: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 43: [ RUN ] AffineTransformationTest.applyTransformationToVectors 43: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 43: [ RUN ] AffineTransformationTest.retrieveGradient 43: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 43: [----------] 3 tests from AffineTransformationTest (0 ms total) 43: 43: [----------] 14 tests from DensitySimilarityTest 43: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 43: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 43: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 43: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 43: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 43: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 43: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 43: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 43: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 43: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 43: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 43: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 43: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (65 ms) 43: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 43: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (65 ms) 43: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 43: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (3 ms) 43: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 43: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (7 ms) 43: [ RUN ] DensitySimilarityTest.NormalizationCorrect 43: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 43: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 43: [----------] 14 tests from DensitySimilarityTest (143 ms total) 43: 43: [----------] 6 tests from StructureSimilarityTest 43: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 43: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 43: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 43: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 43: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 43: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 43: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 43: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 43: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 43: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 43: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 43: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 43: [----------] 6 tests from StructureSimilarityTest (0 ms total) 43: 43: [----------] 8 tests from ExponentialMovingAverage 43: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 43: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 43: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 43: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 43: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 43: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 43: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 43: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 43: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 43: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 43: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 43: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 43: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 43: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 43: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 43: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 43: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 43: 43: [----------] 21 tests from FunctionTest 43: [ RUN ] FunctionTest.StaticLog2 43: [ OK ] FunctionTest.StaticLog2 (0 ms) 43: [ RUN ] FunctionTest.Log2I32Bit 43: [ OK ] FunctionTest.Log2I32Bit (0 ms) 43: [ RUN ] FunctionTest.Log2I64Bit 43: [ OK ] FunctionTest.Log2I64Bit (0 ms) 43: [ RUN ] FunctionTest.GreatestCommonDivisor 43: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 43: [ RUN ] FunctionTest.InvsqrtFloat 43: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 43: [ RUN ] FunctionTest.InvsqrtDouble 43: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 43: [ RUN ] FunctionTest.InvsqrtInteger 43: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 43: [ RUN ] FunctionTest.InvcbrtFloat 43: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 43: [ RUN ] FunctionTest.InvcbrtDouble 43: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 43: [ RUN ] FunctionTest.InvcbrtInteger 43: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 43: [ RUN ] FunctionTest.SixthrootFloat 43: [ OK ] FunctionTest.SixthrootFloat (0 ms) 43: [ RUN ] FunctionTest.SixthrootDouble 43: [ OK ] FunctionTest.SixthrootDouble (1 ms) 43: [ RUN ] FunctionTest.SixthrootInteger 43: [ OK ] FunctionTest.SixthrootInteger (0 ms) 43: [ RUN ] FunctionTest.InvsixthrootFloat 43: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 43: [ RUN ] FunctionTest.InvsixthrootDouble 43: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 43: [ RUN ] FunctionTest.InvsixthrootInteger 43: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 43: [ RUN ] FunctionTest.Powers 43: [ OK ] FunctionTest.Powers (0 ms) 43: [ RUN ] FunctionTest.ErfInvFloat 43: [ OK ] FunctionTest.ErfInvFloat (1 ms) 43: [ RUN ] FunctionTest.ErfInvDouble 43: [ OK ] FunctionTest.ErfInvDouble (0 ms) 43: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 43: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 43: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 43: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 43: [----------] 21 tests from FunctionTest (10 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 43: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 43: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 43: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 43: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 43: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 43: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 43: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 43: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 43: 43: [----------] 4 tests from GaussianOn1DLattice 43: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 43: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 43: [ RUN ] GaussianOn1DLattice.isCorrect 43: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 43: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 43: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 43: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 43: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 43: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 43: 43: [----------] 9 tests from GaussTransformTest 43: [ RUN ] GaussTransformTest.isZeroUponConstruction 43: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 43: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 43: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 43: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 43: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 43: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 43: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 43: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 43: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 43: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 43: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 43: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 43: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 43: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 43: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 43: [ RUN ] GaussTransformTest.view 43: [ OK ] GaussTransformTest.view (0 ms) 43: [----------] 9 tests from GaussTransformTest (0 ms total) 43: 43: [----------] 3 tests from DensityFittingForce 43: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 43: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 43: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 43: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 43: [ RUN ] DensityFittingForce.pullsTowardsDerivative 43: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 43: [----------] 3 tests from DensityFittingForce (0 ms total) 43: 43: [----------] 2 tests from InvertMatrixTest 43: [ RUN ] InvertMatrixTest.IdentityIsImpotent 43: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 43: [ RUN ] InvertMatrixTest.ComputesInverse 43: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 43: [----------] 2 tests from InvertMatrixTest (0 ms total) 43: 43: [----------] 28 tests from MatrixTest 43: [ RUN ] MatrixTest.canSetFromArray 43: [ OK ] MatrixTest.canSetFromArray (0 ms) 43: [ RUN ] MatrixTest.canSetStaticallyFromList 43: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 43: [ RUN ] MatrixTest.canSetStaticallySingleValue 43: [ OK ] MatrixTest.canSetStaticallySingleValue (0 ms) 43: [ RUN ] MatrixTest.canConstructAndFill 43: [ OK ] MatrixTest.canConstructAndFill (0 ms) 43: [ RUN ] MatrixTest.canSetValues 43: [ OK ] MatrixTest.canSetValues (0 ms) 43: [ RUN ] MatrixTest.canCopyAssign 43: [ OK ] MatrixTest.canCopyAssign (0 ms) 43: [ RUN ] MatrixTest.canSwap 43: [ OK ] MatrixTest.canSwap (0 ms) 43: [ RUN ] MatrixTest.staticMultiDimArrayExtent 43: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 43: [ RUN ] MatrixTest.canAddMatrix 43: [ OK ] MatrixTest.canAddMatrix (0 ms) 43: [ RUN ] MatrixTest.canAddAssignMatrix 43: [ OK ] MatrixTest.canAddAssignMatrix (0 ms) 43: [ RUN ] MatrixTest.canSubtractMatrix 43: [ OK ] MatrixTest.canSubtractMatrix (0 ms) 43: [ RUN ] MatrixTest.canSubtractAssignMatrix 43: [ OK ] MatrixTest.canSubtractAssignMatrix (0 ms) 43: [ RUN ] MatrixTest.canNegateMatrix 43: [ OK ] MatrixTest.canNegateMatrix (0 ms) 43: [ RUN ] MatrixTest.MatrixScalarMultiplication 43: [ OK ] MatrixTest.MatrixScalarMultiplication (0 ms) 43: [ RUN ] MatrixTest.MatrixScalarDivision 43: [ OK ] MatrixTest.MatrixScalarDivision (0 ms) 43: [ RUN ] MatrixTest.MatrixVectorMultiplicationOperator 43: [ OK ] MatrixTest.MatrixVectorMultiplicationOperator (0 ms) 43: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 43: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 43: [ RUN ] MatrixTest.MatrixMatrixMultiplication 43: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 43: [ RUN ] MatrixTest.determinantWorks 43: [ OK ] MatrixTest.determinantWorks (0 ms) 43: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 43: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 43: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 43: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 43: [ RUN ] MatrixTest.traceWorks 43: [ OK ] MatrixTest.traceWorks (0 ms) 43: [ RUN ] MatrixTest.transposeWorks 43: [ OK ] MatrixTest.transposeWorks (0 ms) 43: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 43: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 43: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 43: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 43: [ RUN ] MatrixTest.canFillLegacyMatrix 43: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 43: [ RUN ] MatrixTest.IdentityMatrix 43: [ OK ] MatrixTest.IdentityMatrix (0 ms) 43: [ RUN ] MatrixTest.DiagonalMatrix 43: [ OK ] MatrixTest.DiagonalMatrix (0 ms) 43: [----------] 28 tests from MatrixTest (0 ms total) 43: 43: [----------] 25 tests from MultiDimArrayTest 43: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 43: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 43: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 43: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 43: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 43: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 43: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 43: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 43: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 43: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 43: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 43: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 43: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canSwapStatic 43: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canSwapDynamic 43: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 43: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 43: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 43: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 43: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 43: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 43: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 43: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 43: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 43: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 43: [ RUN ] MultiDimArrayTest.conversionToView 43: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 43: [ RUN ] MultiDimArrayTest.conversionToConstView 43: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 43: [ RUN ] MultiDimArrayTest.viewBegin 43: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 43: [ RUN ] MultiDimArrayTest.viewEnd 43: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 43: [ RUN ] MultiDimArrayTest.constViewConstBegin 43: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 43: [ RUN ] MultiDimArrayTest.constViewConstEnd 43: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 43: [----------] 25 tests from MultiDimArrayTest (0 ms total) 43: 43: [----------] 4 tests from MultiDimArrayToMdSpanTest 43: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 43: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 43: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 43: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 43: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 43: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 43: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 43: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 43: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 43: 43: [----------] 9 tests from NelderMeadSimplexTest 43: [ RUN ] NelderMeadSimplexTest.BestVertex 43: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 43: [ RUN ] NelderMeadSimplexTest.WorstVertex 43: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 43: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 43: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 43: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 43: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 43: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 43: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 43: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 43: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 43: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 43: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 43: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 43: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 43: [ RUN ] NelderMeadSimplexTest.OrientedLength 43: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 43: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 43: 43: [----------] 2 tests from NelderMead 43: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 43: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (48 ms) 43: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 43: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 43: [----------] 2 tests from NelderMead (48 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 43: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.ResizeWorks 43: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.ReserveWorks 43: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/0.CanCopyAssign 43: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/0.CanMoveAssign 43: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/0.CanSwap 43: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 43: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.ResizeWorks 43: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.ReserveWorks 43: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/1.CanCopyAssign 43: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/1.CanMoveAssign 43: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/1.CanSwap 43: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 43: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.ResizeWorks 43: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.ReserveWorks 43: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/2.CanCopyAssign 43: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/2.CanMoveAssign 43: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/2.CanSwap 43: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 43: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.ResizeWorks 43: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.ReserveWorks 43: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/3.CanCopyAssign 43: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/3.CanMoveAssign 43: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/3.CanSwap 43: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 43: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.ResizeWorks 43: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.ReserveWorks 43: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/4.CanCopyAssign 43: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/4.CanMoveAssign 43: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/4.CanSwap 43: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 43: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.ResizeWorks 43: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.ReserveWorks 43: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/5.CanCopyAssign 43: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/5.CanMoveAssign 43: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/5.CanSwap 43: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 43: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.ResizeWorks 43: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.ReserveWorks 43: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/6.CanCopyAssign 43: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/6.CanMoveAssign 43: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/6.CanSwap 43: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 43: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.ResizeWorks 43: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.ReserveWorks 43: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/7.CanCopyAssign 43: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/7.CanMoveAssign 43: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/7.CanSwap 43: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 43: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.ResizeWorks 43: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.ReserveWorks 43: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/8.CanCopyAssign 43: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/8.CanMoveAssign 43: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/8.CanSwap 43: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 43: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.ResizeWorks 43: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.ReserveWorks 43: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/9.CanCopyAssign 43: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/9.CanMoveAssign 43: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/9.CanSwap 43: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 293 tests from 40 test suites ran. (210 ms total) 43: [ PASSED ] 293 tests. 43/103 Test #43: MathUnitTests ............................. Passed 0.25 sec test 44 Start 44: MdrunUtilityUnitTests 44: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests 44: Test timeout computed to be: 30 44: [==========] Running 33 tests from 3 test suites. 44: [----------] Global test environment set-up. 44: [----------] 4 tests from MDModulesNotifierTest 44: [ RUN ] MDModulesNotifierTest.AddConsumer 44: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 44: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 44: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 44: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 44: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 44: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 44: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 44: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 44: 44: [----------] 1 test from PlainPairlistRanges 44: [ RUN ] PlainPairlistRanges.RmsdDistance 44: [ OK ] PlainPairlistRanges.RmsdDistance (0 ms) 44: [----------] 1 test from PlainPairlistRanges (0 ms total) 44: 44: [----------] 28 tests from ThreadAffinityTest 44: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 44: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 44: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 44: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 44: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 44: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 44: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 44: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 44: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 44: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 44: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 44: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 44: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 44: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 44: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask 44: [ OK ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 44: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 44: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 44: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 44: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 44: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndFullMask 44: [ OK ] ThreadAffinityTest.PinsWithAffinityAndFullMask (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask 44: [ OK ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask (0 ms) 44: [ RUN ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall 44: [ OK ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithSmt 44: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithSmt (31 ms) 44: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt 44: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt (1 ms) 44: [ RUN ] ThreadAffinityTest.PinsToPCoresInHybridSystem 44: [ OK ] ThreadAffinityTest.PinsToPCoresInHybridSystem (1 ms) 44: [ RUN ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem 44: [ OK ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem (1 ms) 44: [ RUN ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem 44: [ OK ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem (1 ms) 44: [ RUN ] ThreadAffinityTest.PinsToECoresInHybridSystem 44: [ OK ] ThreadAffinityTest.PinsToECoresInHybridSystem (1 ms) 44: [ RUN ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem 44: [ OK ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem (1 ms) 44: [----------] 28 tests from ThreadAffinityTest (44 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 33 tests from 3 test suites ran. (44 ms total) 44: [ PASSED ] 33 tests. 44/103 Test #44: MdrunUtilityUnitTests ..................... Passed 0.07 sec test 45 Start 45: MdrunUtilityMpiUnitTests 45: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdrunutility/tests 45: Test timeout computed to be: 30 45: [==========] Running 17 tests from 2 test suites. 45: [----------] Global test environment set-up. 45: [----------] 10 tests from ThreadAffinityMultiRankTest 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 45: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (14 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 45: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (30 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 45: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (1 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 45: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 45: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (1 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 45: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (1 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent 45: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent (6 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame 45: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame (3 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp 45: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp (6 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken 45: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken (1 ms) 45: [----------] 10 tests from ThreadAffinityMultiRankTest (68 ms total) 45: 45: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (4 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (4 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (3 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (3 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (3 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (4 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (1 ms) 45: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (25 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 17 tests from 2 test suites ran. (93 ms total) 45: [ PASSED ] 17 tests. 45/103 Test #45: MdrunUtilityMpiUnitTests .................. Passed 0.12 sec test 46 Start 46: MDSpanTests 46: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MDSpanTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdspan/tests 46: Test timeout computed to be: 30 46: [==========] Running 32 tests from 7 test suites. 46: [----------] Global test environment set-up. 46: [----------] 4 tests from BasicAccessorPolicy 46: [ RUN ] BasicAccessorPolicy.Decay 46: [ OK ] BasicAccessorPolicy.Decay (0 ms) 46: [ RUN ] BasicAccessorPolicy.Access 46: [ OK ] BasicAccessorPolicy.Access (0 ms) 46: [ RUN ] BasicAccessorPolicy.Offset 46: [ OK ] BasicAccessorPolicy.Offset (0 ms) 46: [ RUN ] BasicAccessorPolicy.CopyAccessor 46: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 46: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 46: 46: [----------] 4 tests from ExtentsTest 46: [ RUN ] ExtentsTest.Construction 46: [ OK ] ExtentsTest.Construction (0 ms) 46: [ RUN ] ExtentsTest.PurelyStatic 46: [ OK ] ExtentsTest.PurelyStatic (0 ms) 46: [ RUN ] ExtentsTest.RankNought 46: [ OK ] ExtentsTest.RankNought (0 ms) 46: [ RUN ] ExtentsTest.Assignment 46: [ OK ] ExtentsTest.Assignment (0 ms) 46: [----------] 4 tests from ExtentsTest (0 ms total) 46: 46: [----------] 8 tests from MdSpanExtension 46: [ RUN ] MdSpanExtension.SlicingAllStatic 46: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 46: [ RUN ] MdSpanExtension.SlicingDynamic 46: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 46: [ RUN ] MdSpanExtension.SlicingAllStatic3D 46: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 46: [ RUN ] MdSpanExtension.SlicingEqualsView3D 46: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 46: [ RUN ] MdSpanExtension.additionWorks 46: [ OK ] MdSpanExtension.additionWorks (0 ms) 46: [ RUN ] MdSpanExtension.subtractionWorks 46: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 46: [ RUN ] MdSpanExtension.multiplicationWorks 46: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 46: [ RUN ] MdSpanExtension.divisionWorks 46: [ OK ] MdSpanExtension.divisionWorks (0 ms) 46: [----------] 8 tests from MdSpanExtension (0 ms total) 46: 46: [----------] 3 tests from LayoutTests 46: [ RUN ] LayoutTests.LayoutRightConstruction 46: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 46: [ RUN ] LayoutTests.LayoutRightProperties 46: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 46: [ RUN ] LayoutTests.LayoutRightOperator 46: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 46: [----------] 3 tests from LayoutTests (0 ms total) 46: 46: [----------] 1 test from MdSpanTest 46: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 46: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 46: [----------] 1 test from MdSpanTest (0 ms total) 46: 46: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 46: [ RUN ] MdSpanTest/0.Rank 46: [ OK ] MdSpanTest/0.Rank (0 ms) 46: [ RUN ] MdSpanTest/0.DynamicRank 46: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 46: [ RUN ] MdSpanTest/0.Extents 46: [ OK ] MdSpanTest/0.Extents (0 ms) 46: [ RUN ] MdSpanTest/0.Strides 46: [ OK ] MdSpanTest/0.Strides (0 ms) 46: [ RUN ] MdSpanTest/0.Properties 46: [ OK ] MdSpanTest/0.Properties (0 ms) 46: [ RUN ] MdSpanTest/0.Operator 46: [ OK ] MdSpanTest/0.Operator (0 ms) 46: [----------] 6 tests from MdSpanTest/0 (0 ms total) 46: 46: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 46: [ RUN ] MdSpanTest/1.Rank 46: [ OK ] MdSpanTest/1.Rank (0 ms) 46: [ RUN ] MdSpanTest/1.DynamicRank 46: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 46: [ RUN ] MdSpanTest/1.Extents 46: [ OK ] MdSpanTest/1.Extents (0 ms) 46: [ RUN ] MdSpanTest/1.Strides 46: [ OK ] MdSpanTest/1.Strides (0 ms) 46: [ RUN ] MdSpanTest/1.Properties 46: [ OK ] MdSpanTest/1.Properties (0 ms) 46: [ RUN ] MdSpanTest/1.Operator 46: [ OK ] MdSpanTest/1.Operator (0 ms) 46: [----------] 6 tests from MdSpanTest/1 (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 32 tests from 7 test suites ran. (0 ms total) 46: [ PASSED ] 32 tests. 46/103 Test #46: MDSpanTests ............................... Passed 0.03 sec test 47 Start 47: MdtypesUnitTest 47: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdtypesUnitTest.xml" 47: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/mdtypes/tests 47: Test timeout computed to be: 30 47: [==========] Running 98 tests from 7 test suites. 47: [----------] Global test environment set-up. 47: [----------] 4 tests from ForeingLambdaTermsDhdl 47: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 47: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 47: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 47: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 47: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 47: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 47: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 47: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 47: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 47: 47: [----------] 4 tests from ObservablesReducerTest 47: [ RUN ] ObservablesReducerTest.CanMoveAssign 47: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 47: [ RUN ] ObservablesReducerTest.CanMoveConstruct 47: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 47: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 47: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 47: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 47: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 47: [----------] 4 tests from ObservablesReducerTest (0 ms total) 47: 47: [----------] 3 tests from CheckpointDataTest 47: [ RUN ] CheckpointDataTest.SingleDataTest 47: [ OK ] CheckpointDataTest.SingleDataTest (39 ms) 47: [ RUN ] CheckpointDataTest.MultiDataTest 47: [ OK ] CheckpointDataTest.MultiDataTest (42 ms) 47: [ RUN ] CheckpointDataTest.EmptyVectorTest 47: [ OK ] CheckpointDataTest.EmptyVectorTest (0 ms) 47: [----------] 3 tests from CheckpointDataTest (82 ms total) 47: 47: [----------] 7 tests from ForceBuffers 47: [ RUN ] ForceBuffers.ConstructsUnpinned 47: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 47: [ RUN ] ForceBuffers.ConstructsPinned 47: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 47: [ RUN ] ForceBuffers.ConstructsEmpty 47: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 47: [ RUN ] ForceBuffers.ResizeWorks 47: [ OK ] ForceBuffers.ResizeWorks (0 ms) 47: [ RUN ] ForceBuffers.PaddingWorks 47: [ OK ] ForceBuffers.PaddingWorks (0 ms) 47: [ RUN ] ForceBuffers.CopyWorks 47: [ OK ] ForceBuffers.CopyWorks (0 ms) 47: [ RUN ] ForceBuffers.CopyDoesNotPin 47: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 47: [----------] 7 tests from ForceBuffers (0 ms total) 47: 47: [----------] 5 tests from MultipleTimeStepping 47: [ RUN ] MultipleTimeStepping.ChecksNumLevels 47: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 47: [ RUN ] MultipleTimeStepping.SelectsForceGroups 47: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 47: [ RUN ] MultipleTimeStepping.ChecksStepFactor 47: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 47: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 47: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 47: [ RUN ] MultipleTimeStepping.ChecksIntegrator 47: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 47: [----------] 5 tests from MultipleTimeStepping (0 ms total) 47: 47: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 47: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (2 ms total) 47: 47: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 47: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 98 tests from 7 test suites ran. (85 ms total) 47: [ PASSED ] 98 tests. 47/103 Test #47: MdtypesUnitTest ........................... Passed 0.11 sec test 48 Start 48: OnlineHelpUnitTests 48: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 48: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/onlinehelp/tests 48: Test timeout computed to be: 30 48: [==========] Running 22 tests from 4 test suites. 48: [----------] Global test environment set-up. 48: [----------] 6 tests from TextTableFormatterTest 48: [ RUN ] TextTableFormatterTest.HandlesBasicCase 48: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 48: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 48: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 48: [ RUN ] TextTableFormatterTest.HandlesIndentation 48: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms) 48: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 48: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms) 48: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 48: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 48: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 48: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (1 ms) 48: [----------] 6 tests from TextTableFormatterTest (7 ms total) 48: 48: [----------] 3 tests from HelpManagerTest 48: [ RUN ] HelpManagerTest.HandlesRootTopic 48: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 48: [ RUN ] HelpManagerTest.HandlesSubTopics 48: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 48: [ RUN ] HelpManagerTest.HandlesInvalidTopics 48: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 48: [----------] 3 tests from HelpManagerTest (0 ms total) 48: 48: [----------] 2 tests from HelpTopicFormattingTest 48: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 48: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 48: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 48: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 48: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 48: 48: [----------] 11 tests from HelpWriterContextTest 48: [ RUN ] HelpWriterContextTest.FormatsParagraphs 48: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 48: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 48: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 48: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsLiteralText 48: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 48: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 48: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsBulletList 48: [ OK ] HelpWriterContextTest.FormatsBulletList (2 ms) 48: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 48: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 48: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms) 48: [ RUN ] HelpWriterContextTest.FormatsGridTable 48: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms) 48: [ RUN ] HelpWriterContextTest.FormatsTitles 48: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 48: [----------] 11 tests from HelpWriterContextTest (8 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 22 tests from 4 test suites ran. (17 ms total) 48: [ PASSED ] 22 tests. 48/103 Test #48: OnlineHelpUnitTests ....................... Passed 0.04 sec test 49 Start 49: OptionsUnitTests 49: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/OptionsUnitTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/options/tests 49: Test timeout computed to be: 30 49: [==========] Running 151 tests from 21 test suites. 49: [----------] Global test environment set-up. 49: [----------] 5 tests from AbstractOptionStorageTest 49: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 49: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 49: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 49: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 49: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 49: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 49: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 49: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 49: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 49: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 49: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 49: 49: [----------] 10 tests from FileNameOptionTest 49: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 49: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 49: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 49: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 49: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 49: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 49: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 49: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 49: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 49: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 49: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 49: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 49: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 49: [----------] 10 tests from FileNameOptionTest (0 ms total) 49: 49: [----------] 16 tests from FileNameOptionManagerTest 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 49: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 49: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 49: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 49: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 49: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 49: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 49: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 49: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 49: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 49: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 49: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 49: [----------] 16 tests from FileNameOptionManagerTest (1 ms total) 49: 49: [----------] 1 test from OptionsTest 49: [ RUN ] OptionsTest.FailsOnNonsafeStorage 49: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 49: [----------] 1 test from OptionsTest (0 ms total) 49: 49: [----------] 9 tests from OptionsAssignerTest 49: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 49: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 49: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 49: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 49: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesMissingValue 49: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesExtraValue 49: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesGroups 49: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesSections 49: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 49: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 49: [----------] 9 tests from OptionsAssignerTest (0 ms total) 49: 49: [----------] 4 tests from OptionsAssignerBooleanTest 49: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 49: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 49: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 49: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 49: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 49: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 49: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 49: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 49: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 49: 49: [----------] 13 tests from OptionsAssignerIntegerTest 49: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 49: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 49: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 49: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 49: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 49: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 49: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 49: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 49: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 49: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 49: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 49: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 49: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 49: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 49: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 49: 49: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet 49: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresToVector 49: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresToVector (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectors 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectors (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 49: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest (0 ms total) 49: 49: [----------] 13 tests from OptionsAssignerInt64Test 49: [ RUN ] OptionsAssignerInt64Test.StoresSingleValue 49: [ OK ] OptionsAssignerInt64Test.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesEmptyValue 49: [ OK ] OptionsAssignerInt64Test.HandlesEmptyValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesInvalidValue 49: [ OK ] OptionsAssignerInt64Test.HandlesInvalidValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesOverflow 49: [ OK ] OptionsAssignerInt64Test.HandlesOverflow (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValue 49: [ OK ] OptionsAssignerInt64Test.StoresDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValueIfSet 49: [ OK ] OptionsAssignerInt64Test.StoresDefaultValueIfSet (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet 49: [ OK ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesBothDefaultValues 49: [ OK ] OptionsAssignerInt64Test.HandlesBothDefaultValues (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.StoresToVector 49: [ OK ] OptionsAssignerInt64Test.StoresToVector (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesVectors 49: [ OK ] OptionsAssignerInt64Test.HandlesVectors (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue 49: [ OK ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue 49: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 49: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 49: [----------] 13 tests from OptionsAssignerInt64Test (0 ms total) 49: 49: [----------] 13 tests from OptionsAssignerUnsignedInt64Test 49: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresSingleValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesOverflow 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesOverflow (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet 49: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresToVector 49: [ OK ] OptionsAssignerUnsignedInt64Test.StoresToVector (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectors 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectors (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 49: [----------] 13 tests from OptionsAssignerUnsignedInt64Test (0 ms total) 49: 49: [----------] 5 tests from OptionsAssignerDoubleTest 49: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 49: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 49: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 49: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 49: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 49: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 49: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 49: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 49: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 49: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 49: 49: [----------] 9 tests from OptionsAssignerStringTest 49: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 49: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 49: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 49: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 49: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 49: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 49: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 49: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 49: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 49: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 49: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 49: 49: [----------] 6 tests from OptionsAssignerEnumTest 49: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 49: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 49: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 49: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 49: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 49: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 49: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 49: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 49: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 49: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 49: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 49: 49: [----------] 8 tests from RepeatingOptionSectionTest 49: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 49: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 49: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 49: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 49: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 49: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 49: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 49: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 49: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 49: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 49: 49: [----------] 1 test from TimeUnitManagerTest 49: [ RUN ] TimeUnitManagerTest.BasicOperations 49: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 49: [----------] 1 test from TimeUnitManagerTest (0 ms total) 49: 49: [----------] 4 tests from TimeUnitBehaviorTest 49: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 49: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 49: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 49: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 49: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 49: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 49: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 49: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 49: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 49: 49: [----------] 2 tests from TreeValueSupportAssignTest 49: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 49: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 49: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 49: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 49: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 49: 49: [----------] 1 test from TreeValueSupportAssignErrorTest 49: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 49: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 49: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 49: 49: [----------] 5 tests from TreeValueSupportCheckTest 49: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 49: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 49: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 49: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 49: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 49: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 49: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 49: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 49: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 49: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 49: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 49: 49: [----------] 6 tests from TreeValueSupportAdjustTest 49: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 49: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (3 ms) 49: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 49: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms) 49: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 49: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms) 49: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 49: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 49: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 49: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (1 ms) 49: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 49: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 49: [----------] 6 tests from TreeValueSupportAdjustTest (9 ms total) 49: 49: [----------] 7 tests from TreeValueSupportTest 49: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 49: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms) 49: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 49: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms) 49: [ RUN ] TreeValueSupportTest.SupportsInt64Option 49: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms) 49: [ RUN ] TreeValueSupportTest.SupportsStringOption 49: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 49: [ RUN ] TreeValueSupportTest.SupportsFloatOption 49: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 49: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 49: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 49: [ RUN ] TreeValueSupportTest.SupportsEnumOption 49: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 49: [----------] 7 tests from TreeValueSupportTest (7 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 151 tests from 21 test suites ran. (24 ms total) 49: [ PASSED ] 151 tests. 49/103 Test #49: OptionsUnitTests .......................... Passed 0.06 sec test 50 Start 50: PbcutilUnitTest 50: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pbcutil/tests 50: Test timeout computed to be: 30 50: [==========] Running 36 tests from 5 test suites. 50: [----------] Global test environment set-up. 50: [----------] 1 test from ShiftTest 50: [ RUN ] ShiftTest.CoordinateShiftWorks 50: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 50: [----------] 1 test from ShiftTest (0 ms total) 50: 50: [----------] 2 tests from MShift 50: [ RUN ] MShift.shiftsAndUnshifts 50: [ OK ] MShift.shiftsAndUnshifts (0 ms) 50: [ RUN ] MShift.shiftsAndUnshiftsSelf 50: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 50: [----------] 2 tests from MShift (0 ms total) 50: 50: [----------] 4 tests from PbcTest 50: [ RUN ] PbcTest.CalcShiftsWorks 50: [ OK ] PbcTest.CalcShiftsWorks (3 ms) 50: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 50: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 50: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 50: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 50: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 50: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 50: [----------] 4 tests from PbcTest (3 ms total) 50: 50: [----------] 2 tests from PbcEnumsTest 50: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 50: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 50: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 50: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 50: [----------] 2 tests from PbcEnumsTest (0 ms total) 50: 50: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (1 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (2 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (2 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (1 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (2 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (2 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (1 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (1 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 50: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (28 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 36 tests from 5 test suites ran. (32 ms total) 50: [ PASSED ] 36 tests. 50/103 Test #50: PbcutilUnitTest ........................... Passed 0.06 sec test 51 Start 51: RandomUnitTests 51: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/RandomUnitTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/random/tests 51: Test timeout computed to be: 30 51: [==========] Running 44 tests from 10 test suites. 51: [----------] Global test environment set-up. 51: [----------] 4 tests from ExponentialDistributionTest 51: [ RUN ] ExponentialDistributionTest.Output 51: [ OK ] ExponentialDistributionTest.Output (0 ms) 51: [ RUN ] ExponentialDistributionTest.Logical 51: [ OK ] ExponentialDistributionTest.Logical (0 ms) 51: [ RUN ] ExponentialDistributionTest.Reset 51: [ OK ] ExponentialDistributionTest.Reset (0 ms) 51: [ RUN ] ExponentialDistributionTest.AltParam 51: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 51: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 51: 51: [----------] 4 tests from GammaDistributionTest 51: [ RUN ] GammaDistributionTest.Output 51: [ OK ] GammaDistributionTest.Output (2 ms) 51: [ RUN ] GammaDistributionTest.Logical 51: [ OK ] GammaDistributionTest.Logical (0 ms) 51: [ RUN ] GammaDistributionTest.Reset 51: [ OK ] GammaDistributionTest.Reset (0 ms) 51: [ RUN ] GammaDistributionTest.AltParam 51: [ OK ] GammaDistributionTest.AltParam (0 ms) 51: [----------] 4 tests from GammaDistributionTest (2 ms total) 51: 51: [----------] 4 tests from NormalDistributionTest 51: [ RUN ] NormalDistributionTest.Output 51: [ OK ] NormalDistributionTest.Output (0 ms) 51: [ RUN ] NormalDistributionTest.Logical 51: [ OK ] NormalDistributionTest.Logical (0 ms) 51: [ RUN ] NormalDistributionTest.Reset 51: [ OK ] NormalDistributionTest.Reset (0 ms) 51: [ RUN ] NormalDistributionTest.AltParam 51: [ OK ] NormalDistributionTest.AltParam (0 ms) 51: [----------] 4 tests from NormalDistributionTest (0 ms total) 51: 51: [----------] 1 test from SeedTest 51: [ RUN ] SeedTest.makeRandomSeed 51: [ OK ] SeedTest.makeRandomSeed (0 ms) 51: [----------] 1 test from SeedTest (0 ms total) 51: 51: [----------] 6 tests from TabulatedNormalDistributionTest 51: [ RUN ] TabulatedNormalDistributionTest.Output14 51: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 51: [ RUN ] TabulatedNormalDistributionTest.Output16 51: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 51: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 51: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 51: [ RUN ] TabulatedNormalDistributionTest.Logical 51: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 51: [ RUN ] TabulatedNormalDistributionTest.Reset 51: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 51: [ RUN ] TabulatedNormalDistributionTest.AltParam 51: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 51: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) 51: 51: [----------] 1 test from TabulatedNormalDistributionTableTest 51: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 51: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 51: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 51: 51: [----------] 6 tests from ThreeFry2x64Test 51: [ RUN ] ThreeFry2x64Test.Logical 51: [ OK ] ThreeFry2x64Test.Logical (0 ms) 51: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 51: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 51: [ RUN ] ThreeFry2x64Test.Reseed 51: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 51: [ RUN ] ThreeFry2x64Test.Discard 51: [ OK ] ThreeFry2x64Test.Discard (0 ms) 51: [ RUN ] ThreeFry2x64Test.InvalidCounter 51: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 51: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 51: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 51: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 51: 51: [----------] 4 tests from UniformIntDistributionTest 51: [ RUN ] UniformIntDistributionTest.Output 51: [ OK ] UniformIntDistributionTest.Output (0 ms) 51: [ RUN ] UniformIntDistributionTest.Logical 51: [ OK ] UniformIntDistributionTest.Logical (0 ms) 51: [ RUN ] UniformIntDistributionTest.Reset 51: [ OK ] UniformIntDistributionTest.Reset (0 ms) 51: [ RUN ] UniformIntDistributionTest.AltParam 51: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 51: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 51: 51: [----------] 5 tests from UniformRealDistributionTest 51: [ RUN ] UniformRealDistributionTest.GenerateCanonical 51: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 51: [ RUN ] UniformRealDistributionTest.Output 51: [ OK ] UniformRealDistributionTest.Output (0 ms) 51: [ RUN ] UniformRealDistributionTest.Logical 51: [ OK ] UniformRealDistributionTest.Logical (0 ms) 51: [ RUN ] UniformRealDistributionTest.Reset 51: [ OK ] UniformRealDistributionTest.Reset (0 ms) 51: [ RUN ] UniformRealDistributionTest.AltParam 51: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 51: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 51: 51: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 51: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (4 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 44 tests from 10 test suites ran. (11 ms total) 51: [ PASSED ] 44 tests. 51/103 Test #51: RandomUnitTests ........................... Passed 0.04 sec test 52 Start 52: RestraintTests 52: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/RestraintTests.xml" 52: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/restraint/tests 52: Test timeout computed to be: 30 52: [==========] Running 1 test from 1 test suite. 52: [----------] Global test environment set-up. 52: [----------] 1 test from RestraintManager 52: [ RUN ] RestraintManager.restraintList 52: [ OK ] RestraintManager.restraintList (0 ms) 52: [----------] 1 test from RestraintManager (0 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 1 test from 1 test suite ran. (0 ms total) 52: [ PASSED ] 1 test. 52/103 Test #52: RestraintTests ............................ Passed 0.02 sec test 53 Start 53: SerializationUnitTests 53: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/serialization-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/SerializationUnitTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/serialization/tests 53: Test timeout computed to be: 30 53: [==========] Running 9 tests from 2 test suites. 53: [----------] Global test environment set-up. 53: [----------] 5 tests from InMemorySerializerTest 53: [ RUN ] InMemorySerializerTest.Roundtrip 53: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 53: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 53: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 53: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 53: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 53: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 53: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 53: [ RUN ] InMemorySerializerTest.SizeIsCorrect 53: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 53: [----------] 5 tests from InMemorySerializerTest (0 ms total) 53: 53: [----------] 4 tests from KeyValueTreeSerializerTest 53: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 53: [ OK ] KeyValueTreeSerializerTest.EmptyTree (6 ms) 53: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 53: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 53: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 53: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 53: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 53: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 53: [----------] 4 tests from KeyValueTreeSerializerTest (8 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 9 tests from 2 test suites ran. (9 ms total) 53: [ PASSED ] 9 tests. 53/103 Test #53: SerializationUnitTests .................... Passed 0.03 sec test 54 Start 54: TableUnitTests 54: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/TableUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tables/tests 54: Test timeout computed to be: 30 54: [==========] Running 16 tests from 2 test suites. 54: [----------] Global test environment set-up. 54: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 54: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 54: [ OK ] SplineTableTest/0.HandlesIncorrectInput (2 ms) 54: [ RUN ] SplineTableTest/0.Sinc 54: [ OK ] SplineTableTest/0.Sinc (0 ms) 54: [ RUN ] SplineTableTest/0.LJ12 54: [ OK ] SplineTableTest/0.LJ12 (13 ms) 54: [ RUN ] SplineTableTest/0.PmeCorrection 54: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 54: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 54: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 54: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 54: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 54: [ RUN ] SplineTableTest/0.TwoFunctions 54: [ OK ] SplineTableTest/0.TwoFunctions (25 ms) 54: [ RUN ] SplineTableTest/0.ThreeFunctions 54: [ OK ] SplineTableTest/0.ThreeFunctions (29 ms) 54: [----------] 8 tests from SplineTableTest/0 (75 ms total) 54: 54: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 54: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 54: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 54: [ RUN ] SplineTableTest/1.Sinc 54: [ OK ] SplineTableTest/1.Sinc (0 ms) 54: [ RUN ] SplineTableTest/1.LJ12 54: [ OK ] SplineTableTest/1.LJ12 (1 ms) 54: [ RUN ] SplineTableTest/1.PmeCorrection 54: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 54: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 54: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 54: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 54: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (1 ms) 54: [ RUN ] SplineTableTest/1.TwoFunctions 54: [ OK ] SplineTableTest/1.TwoFunctions (3 ms) 54: [ RUN ] SplineTableTest/1.ThreeFunctions 54: [ OK ] SplineTableTest/1.ThreeFunctions (4 ms) 54: [----------] 8 tests from SplineTableTest/1 (16 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 16 tests from 2 test suites ran. (91 ms total) 54: [ PASSED ] 16 tests. 54/103 Test #54: TableUnitTests ............................ Passed 0.12 sec test 55 Start 55: TaskAssignmentUnitTests 55: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/taskassignment/tests 55: Test timeout computed to be: 30 55: [==========] Running 3 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 55: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 55: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 55: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 55: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 55: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 55: 55: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 55: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 55: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 55: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 3 tests from 2 test suites ran. (1 ms total) 55: [ PASSED ] 3 tests. 55/103 Test #55: TaskAssignmentUnitTests ................... Passed 0.03 sec test 56 Start 56: GmxTimingTests 56: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/GmxTimingTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/timing/tests 56: Test timeout computed to be: 30 56: [==========] Running 6 tests from 1 test suite. 56: [----------] Global test environment set-up. 56: [----------] 6 tests from TimingTest 56: [ RUN ] TimingTest.ElementCountingWorks 56: [ OK ] TimingTest.ElementCountingWorks (0 ms) 56: [ RUN ] TimingTest.ElementNoCountingWorks 56: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 56: [ RUN ] TimingTest.SubElementCountingWorks 56: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 56: [ RUN ] TimingTest.SubElementNoCountingWorks 56: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 56: [ RUN ] TimingTest.RunWallCycle 56: [ OK ] TimingTest.RunWallCycle (1 ms) 56: [ RUN ] TimingTest.RunWallCycleSub 56: [ OK ] TimingTest.RunWallCycleSub (0 ms) 56: [----------] 6 tests from TimingTest (1 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 6 tests from 1 test suite ran. (1 ms total) 56: [ PASSED ] 6 tests. 56/103 Test #56: GmxTimingTests ............................ Passed 0.02 sec test 57 Start 57: TopologyTest 57: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/TopologyTest.xml" 57: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/topology/tests 57: Test timeout computed to be: 30 57: [==========] Running 153 tests from 10 test suites. 57: [----------] Global test environment set-up. 57: [----------] 3 tests from PdbAtomEntryTest 57: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 57: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 57: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 57: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 57: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 57: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 57: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 57: 57: [----------] 3 tests from ExclusionBlockTest 57: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 57: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 57: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 57: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 57: [ RUN ] ExclusionBlockTest.MergeExclusions 57: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 57: [----------] 3 tests from ExclusionBlockTest (0 ms total) 57: 57: [----------] 6 tests from InteractionListTest 57: [ RUN ] InteractionListTest.EmptyWorks 57: [ OK ] InteractionListTest.EmptyWorks (0 ms) 57: [ RUN ] InteractionListTest.CanAddInteractionArray 57: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 57: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 57: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 57: [ RUN ] InteractionListTest.CanAddInteractionPointer 57: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 57: [ RUN ] InteractionListTest.CanAddListToOtherList 57: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 57: [ RUN ] InteractionListTest.ClearingWorks 57: [ OK ] InteractionListTest.ClearingWorks (0 ms) 57: [----------] 6 tests from InteractionListTest (0 ms total) 57: 57: [----------] 3 tests from IndexTest 57: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: The atomic radii are set according to: 57: 57: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 57: A. Bondi 57: van der Waals Volumes and Radii 57: J. Phys. Chem. (1964) 57: https://doi.org/10.1021/j100785a001 57: -------- -------- --- Thank You --- -------- -------- 57: 57: [ OK ] IndexTest.AnalyseWorksDefaultGroups (43 ms) 57: [ RUN ] IndexTest.WriteIndexWorks 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: The atomic radii are set according to: 57: 57: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 57: A. Bondi 57: van der Waals Volumes and Radii 57: J. Phys. Chem. (1964) 57: https://doi.org/10.1021/j100785a001 57: -------- -------- --- Thank You --- -------- -------- 57: 57: [ OK ] IndexTest.WriteIndexWorks (5 ms) 57: [ RUN ] IndexTest.WriteAndReadIndexWorks 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: The atomic radii are set according to: 57: 57: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 57: A. Bondi 57: van der Waals Volumes and Radii 57: J. Phys. Chem. (1964) 57: https://doi.org/10.1021/j100785a001 57: -------- -------- --- Thank You --- -------- -------- 57: 57: [ OK ] IndexTest.WriteAndReadIndexWorks (5 ms) 57: [----------] 3 tests from IndexTest (54 ms total) 57: 57: [----------] 4 tests from MtopTest 57: [ RUN ] MtopTest.RangeBasedLoop 57: [ OK ] MtopTest.RangeBasedLoop (0 ms) 57: [ RUN ] MtopTest.Operators 57: [ OK ] MtopTest.Operators (0 ms) 57: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 57: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 57: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 57: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 57: [----------] 4 tests from MtopTest (0 ms total) 57: 57: [----------] 2 tests from IListRangeTest 57: [ RUN ] IListRangeTest.RangeBasedLoopWorks 57: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 57: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 57: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 57: [----------] 2 tests from IListRangeTest (0 ms total) 57: 57: [----------] 13 tests from StringTableTest 57: [ RUN ] StringTableTest.AddSingleEntry 57: [ OK ] StringTableTest.AddSingleEntry (0 ms) 57: [ RUN ] StringTableTest.CanAccessWithAt 57: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 57: [ RUN ] StringTableTest.CanAccessWithBracket 57: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 57: [ RUN ] StringTableTest.ThrowsOutOfRange 57: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 57: [ RUN ] StringTableTest.StringCompareIsCorrect 57: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 57: [ RUN ] StringTableTest.AddTwoDistinctEntries 57: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 57: [ RUN ] StringTableTest.TryToAddDuplicates 57: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 57: [ RUN ] StringTableTest.AddLargeNumberOfEntries 57: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 57: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 57: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 57: [ RUN ] StringTableTest.CanWriteToBuffer 57: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 57: [ RUN ] StringTableTest.Roundtrip 57: [ OK ] StringTableTest.Roundtrip (0 ms) 57: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 57: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 57: [ RUN ] StringTableTest.CanCopyToLegacyTable 57: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 57: [----------] 13 tests from StringTableTest (5 ms total) 57: 57: [----------] 6 tests from LegacySymtabTest 57: [ RUN ] LegacySymtabTest.EmptyOnOpen 57: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 57: [ RUN ] LegacySymtabTest.AddSingleEntry 57: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 57: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 57: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 57: [ RUN ] LegacySymtabTest.TryToAddDuplicates 57: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 57: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 57: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 57: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 57: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 57: [----------] 6 tests from LegacySymtabTest (0 ms total) 57: 57: [----------] 5 tests from TopSortTest 57: [ RUN ] TopSortTest.WorksOnEmptyIdef 57: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 57: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 57: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 57: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 57: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 57: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 57: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 57: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 57: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 57: [----------] 5 tests from TopSortTest (0 ms total) 57: 57: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 57: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (39 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 153 tests from 10 test suites ran. (101 ms total) 57: [ PASSED ] 153 tests. 57: 57: YOU HAVE 1 DISABLED TEST 57: 57/103 Test #57: TopologyTest .............................. Passed 0.13 sec test 58 Start 58: PullTest 58: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/PullTest.xml" 58: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/pulling/tests 58: Test timeout computed to be: 30 58: [==========] Running 10 tests from 1 test suite. 58: [----------] Global test environment set-up. 58: [----------] 10 tests from PullTest 58: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 58: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 58: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 58: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 58: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 58: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 58: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 58: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 58: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 58: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 58: [ RUN ] PullTest.TransformationCoordSimple 58: [ OK ] PullTest.TransformationCoordSimple (0 ms) 58: [ RUN ] PullTest.TransformationCoordAdvanced 58: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 58: [ RUN ] PullTest.TransformationCoordTime 58: [ OK ] PullTest.TransformationCoordTime (0 ms) 58: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 58: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 58: [ RUN ] PullTest.TransformationCoordDummyExpression 58: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 58: [----------] 10 tests from PullTest (1 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 10 tests from 1 test suite ran. (1 ms total) 58: [ PASSED ] 10 tests. 58/103 Test #58: PullTest .................................. Passed 0.03 sec test 59 Start 59: SimdUnitTests 59: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/SimdUnitTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/simd/tests 59: Test timeout computed to be: 30 59: [==========] Running 86 tests from 3 test suites. 59: [----------] Global test environment set-up. 59: [----------] 41 tests from SimdScalarTest 59: [ RUN ] SimdScalarTest.load 59: [ OK ] SimdScalarTest.load (0 ms) 59: [ RUN ] SimdScalarTest.loadU 59: [ OK ] SimdScalarTest.loadU (0 ms) 59: [ RUN ] SimdScalarTest.store 59: [ OK ] SimdScalarTest.store (0 ms) 59: [ RUN ] SimdScalarTest.storeU 59: [ OK ] SimdScalarTest.storeU (0 ms) 59: [ RUN ] SimdScalarTest.setZero 59: [ OK ] SimdScalarTest.setZero (0 ms) 59: [ RUN ] SimdScalarTest.andNot 59: [ OK ] SimdScalarTest.andNot (0 ms) 59: [ RUN ] SimdScalarTest.fma 59: [ OK ] SimdScalarTest.fma (0 ms) 59: [ RUN ] SimdScalarTest.fms 59: [ OK ] SimdScalarTest.fms (0 ms) 59: [ RUN ] SimdScalarTest.fnma 59: [ OK ] SimdScalarTest.fnma (0 ms) 59: [ RUN ] SimdScalarTest.fnms 59: [ OK ] SimdScalarTest.fnms (0 ms) 59: [ RUN ] SimdScalarTest.maskAdd 59: [ OK ] SimdScalarTest.maskAdd (0 ms) 59: [ RUN ] SimdScalarTest.maskzMul 59: [ OK ] SimdScalarTest.maskzMul (0 ms) 59: [ RUN ] SimdScalarTest.maskzFma 59: [ OK ] SimdScalarTest.maskzFma (0 ms) 59: [ RUN ] SimdScalarTest.abs 59: [ OK ] SimdScalarTest.abs (0 ms) 59: [ RUN ] SimdScalarTest.max 59: [ OK ] SimdScalarTest.max (0 ms) 59: [ RUN ] SimdScalarTest.min 59: [ OK ] SimdScalarTest.min (0 ms) 59: [ RUN ] SimdScalarTest.round 59: [ OK ] SimdScalarTest.round (0 ms) 59: [ RUN ] SimdScalarTest.trunc 59: [ OK ] SimdScalarTest.trunc (0 ms) 59: [ RUN ] SimdScalarTest.reduce 59: [ OK ] SimdScalarTest.reduce (0 ms) 59: [ RUN ] SimdScalarTest.testBits 59: [ OK ] SimdScalarTest.testBits (0 ms) 59: [ RUN ] SimdScalarTest.anyTrue 59: [ OK ] SimdScalarTest.anyTrue (0 ms) 59: [ RUN ] SimdScalarTest.selectByMask 59: [ OK ] SimdScalarTest.selectByMask (0 ms) 59: [ RUN ] SimdScalarTest.selectByNotMask 59: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 59: [ RUN ] SimdScalarTest.blend 59: [ OK ] SimdScalarTest.blend (0 ms) 59: [ RUN ] SimdScalarTest.cvtR2I 59: [ OK ] SimdScalarTest.cvtR2I (0 ms) 59: [ RUN ] SimdScalarTest.cvttR2I 59: [ OK ] SimdScalarTest.cvttR2I (0 ms) 59: [ RUN ] SimdScalarTest.cvtI2R 59: [ OK ] SimdScalarTest.cvtI2R (0 ms) 59: [ RUN ] SimdScalarTest.cvtF2D 59: [ OK ] SimdScalarTest.cvtF2D (0 ms) 59: [ RUN ] SimdScalarTest.cvtD2D 59: [ OK ] SimdScalarTest.cvtD2D (0 ms) 59: [ RUN ] SimdScalarTest.loadI 59: [ OK ] SimdScalarTest.loadI (0 ms) 59: [ RUN ] SimdScalarTest.loadUI 59: [ OK ] SimdScalarTest.loadUI (0 ms) 59: [ RUN ] SimdScalarTest.storeI 59: [ OK ] SimdScalarTest.storeI (0 ms) 59: [ RUN ] SimdScalarTest.storeUI 59: [ OK ] SimdScalarTest.storeUI (0 ms) 59: [ RUN ] SimdScalarTest.andNotI 59: [ OK ] SimdScalarTest.andNotI (0 ms) 59: [ RUN ] SimdScalarTest.testBitsI 59: [ OK ] SimdScalarTest.testBitsI (0 ms) 59: [ RUN ] SimdScalarTest.selectByMaskI 59: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 59: [ RUN ] SimdScalarTest.selectByNotMaskI 59: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 59: [ RUN ] SimdScalarTest.blendI 59: [ OK ] SimdScalarTest.blendI (0 ms) 59: [ RUN ] SimdScalarTest.cvtB2IB 59: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 59: [ RUN ] SimdScalarTest.cvtIB2B 59: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 59: [ RUN ] SimdScalarTest.expandScalarsToTriplets 59: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 59: [----------] 41 tests from SimdScalarTest (0 ms total) 59: 59: [----------] 8 tests from SimdScalarUtilTest 59: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 59: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 59: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 59: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 59: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 59: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 59: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 59: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 59: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 59: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 59: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 59: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 59: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 59: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 59: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 59: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 59: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 59: 59: [----------] 37 tests from SimdScalarMathTest 59: [ RUN ] SimdScalarMathTest.copysign 59: [ OK ] SimdScalarMathTest.copysign (0 ms) 59: [ RUN ] SimdScalarMathTest.invsqrtPair 59: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 59: [ RUN ] SimdScalarMathTest.inv 59: [ OK ] SimdScalarMathTest.inv (0 ms) 59: [ RUN ] SimdScalarMathTest.maskzInvsqrt 59: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 59: [ RUN ] SimdScalarMathTest.log 59: [ OK ] SimdScalarMathTest.log (0 ms) 59: [ RUN ] SimdScalarMathTest.exp2 59: [ OK ] SimdScalarMathTest.exp2 (0 ms) 59: [ RUN ] SimdScalarMathTest.exp 59: [ OK ] SimdScalarMathTest.exp (0 ms) 59: [ RUN ] SimdScalarMathTest.erf 59: [ OK ] SimdScalarMathTest.erf (0 ms) 59: [ RUN ] SimdScalarMathTest.erfc 59: [ OK ] SimdScalarMathTest.erfc (0 ms) 59: [ RUN ] SimdScalarMathTest.sincos 59: [ OK ] SimdScalarMathTest.sincos (0 ms) 59: [ RUN ] SimdScalarMathTest.sin 59: [ OK ] SimdScalarMathTest.sin (0 ms) 59: [ RUN ] SimdScalarMathTest.cos 59: [ OK ] SimdScalarMathTest.cos (0 ms) 59: [ RUN ] SimdScalarMathTest.tan 59: [ OK ] SimdScalarMathTest.tan (0 ms) 59: [ RUN ] SimdScalarMathTest.asin 59: [ OK ] SimdScalarMathTest.asin (0 ms) 59: [ RUN ] SimdScalarMathTest.acos 59: [ OK ] SimdScalarMathTest.acos (0 ms) 59: [ RUN ] SimdScalarMathTest.atan 59: [ OK ] SimdScalarMathTest.atan (0 ms) 59: [ RUN ] SimdScalarMathTest.atan2 59: [ OK ] SimdScalarMathTest.atan2 (0 ms) 59: [ RUN ] SimdScalarMathTest.pmeForceCorrection 59: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 59: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 59: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 59: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 59: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.invSingleAccuracy 59: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 59: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.logSingleAccuracy 59: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 59: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.expSingleAccuracy 59: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 59: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 59: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 59: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 59: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 59: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 59: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 59: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 59: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 59: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 59: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 59: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 59: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 59: [----------] 37 tests from SimdScalarMathTest (0 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 86 tests from 3 test suites ran. (1 ms total) 59: [ PASSED ] 86 tests. 59/103 Test #59: SimdUnitTests ............................. Passed 0.03 sec test 60 Start 60: CompatibilityHelpersTests 60: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/compat/tests 60: Test timeout computed to be: 30 60: [==========] Running 9 tests from 6 test suites. 60: [----------] Global test environment set-up. 60: [----------] 4 tests from TemplateMPTest 60: [ RUN ] TemplateMPTest.MpWithIndexInt 60: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 60: [ RUN ] TemplateMPTest.MpWithIndexIntBad 60: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 60: [ RUN ] TemplateMPTest.MpWithIndexBool 60: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 60: [ RUN ] TemplateMPTest.MpWithIndexEnum 60: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 60: [----------] 4 tests from TemplateMPTest (0 ms total) 60: 60: [----------] 1 test from NotNullConstruction 60: [ RUN ] NotNullConstruction.Works 60: [ OK ] NotNullConstruction.Works (0 ms) 60: [----------] 1 test from NotNullConstruction (0 ms total) 60: 60: [----------] 1 test from NotNullCasting 60: [ RUN ] NotNullCasting.Works 60: [ OK ] NotNullCasting.Works (0 ms) 60: [----------] 1 test from NotNullCasting (0 ms total) 60: 60: [----------] 1 test from NotNullAssignment 60: [ RUN ] NotNullAssignment.Works 60: [ OK ] NotNullAssignment.Works (0 ms) 60: [----------] 1 test from NotNullAssignment (0 ms total) 60: 60: [----------] 1 test from MakeNotNull 60: [ RUN ] MakeNotNull.Works 60: [ OK ] MakeNotNull.Works (0 ms) 60: [----------] 1 test from MakeNotNull (0 ms total) 60: 60: [----------] 1 test from NotNull 60: [ RUN ] NotNull.WorksInContainers 60: [ OK ] NotNull.WorksInContainers (0 ms) 60: [----------] 1 test from NotNull (0 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 9 tests from 6 test suites ran. (0 ms total) 60: [ PASSED ] 9 tests. 60/103 Test #60: CompatibilityHelpersTests ................. Passed 0.02 sec test 61 Start 61: GmxAnaTest 61: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/GmxAnaTest.xml" 61: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests 61: Test timeout computed to be: 600 61: [==========] Running 37 tests from 10 test suites. 61: [----------] Global test environment set-up. 61: [----------] 7 tests from Entropy 61: [ RUN ] Entropy.Schlitter_300_NoLinear 61: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 61: [ RUN ] Entropy.Schlitter_300_Linear 61: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 61: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 61: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 61: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 61: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 61: [ RUN ] Entropy.QuasiHarmonic_200_Linear 61: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 61: [ RUN ] Entropy.EntropyCompare_200_Linear 61: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 61: [ RUN ] Entropy.EntropyCompare_300_Linear 61: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 61: [----------] 7 tests from Entropy (2 ms total) 61: 61: [----------] 2 tests from GmxChiTest 61: [ RUN ] GmxChiTest.gmxchiWorksWithAll 61: Analyzing from residue 1 to residue 11 61: 10 residues with dihedrals found 61: 46 dihedrals found 61: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 61: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 61: j after resetting (nr. active dihedrals) = 46 61: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 61: Now calculating transitions... 61: Total number of transitions: 0 61: Now printing out transitions and OPs... 61: Now printing out rotamer occupancies... 61: Now calculating Chi product trajectories... 61: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 61: [ OK ] GmxChiTest.gmxchiWorksWithAll (1702 ms) 61: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 61: Analyzing from residue 2 to residue 6 61: 5 residues with dihedrals found 61: 23 dihedrals found 61: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 61: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 61: j after resetting (nr. active dihedrals) = 23 61: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 61: Now calculating transitions... 61: Total number of transitions: 0 61: Now printing out transitions and OPs... 61: Now printing out rotamer occupancies... 61: Now calculating Chi product trajectories... 61: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 61: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (896 ms) 61: [----------] 2 tests from GmxChiTest (3043 ms total) 61: 61: [----------] 10 tests from MindistTest 61: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 0: 'atom1' 61: Selected 1: 'atom2' 61: [ OK ] MindistTest.mindistWorksWithSingleAtoms (2634 ms) 61: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 2: 'atom3' 61: Selected 3: 'atoms12' 61: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (24 ms) 61: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 0: 'atom1' 61: Selected 1: 'atom2' 61: [ OK ] MindistTest.mindistDoesNotPickUpContacts (79 ms) 61: [ RUN ] MindistTest.mindistPicksUpContacts 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 0: 'atom1' 61: Selected 1: 'atom2' 61: [ OK ] MindistTest.mindistPicksUpContacts (294 ms) 61: [ RUN ] MindistTest.ngWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 0: 'atom1' 61: Selected 1: 'atom2' 61: Selected 2: 'atom3' 61: [ OK ] MindistTest.ngWorks (33 ms) 61: [ RUN ] MindistTest.groupWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 3: 'atoms12' 61: Selected 2: 'atom3' 61: [ OK ] MindistTest.groupWorks (188 ms) 61: [ RUN ] MindistTest.maxDistWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 2: 'atom3' 61: Selected 3: 'atoms12' 61: [ OK ] MindistTest.maxDistWorks (11 ms) 61: [ RUN ] MindistTest.noPbcWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 0: 'atom1' 61: Selected 1: 'atom2' 61: [ OK ] MindistTest.noPbcWorks (32 ms) 61: [ RUN ] MindistTest.resPerTimeWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 3: 'atoms12' 61: Selected 2: 'atom3' 61: [ OK ] MindistTest.resPerTimeWorks (159 ms) 61: [ RUN ] MindistTest.matrixWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 5: 'atoms123' 61: Special case: making distance matrix between all atoms in group atoms123 61: [ OK ] MindistTest.matrixWorks (33 ms) 61: [----------] 10 tests from MindistTest (3493 ms total) 61: 61: [----------] 1 test from GmxRmsTest 61: [ RUN ] GmxRmsTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Select group for least squares fit 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Select group for RMSD calculation 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 61: Setting the LD random seed to -1309147561 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 1: 'Protein' 61: Selected 1: 'Protein' 61: [ OK ] GmxRmsTest.BasicOutputWorks (1933 ms) 61: [----------] 1 test from GmxRmsTest (1933 ms total) 61: 61: [----------] 1 test from GmxRmsdistTest 61: [ RUN ] GmxRmsdistTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 61: 61: rmsmax = 0.382568, rmscmax = 0.659498 61: Setting the LD random seed to 250346475 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 0: 'System' 61: [ OK ] GmxRmsdistTest.BasicOutputWorks (1100 ms) 61: [----------] 1 test from GmxRmsdistTest (1100 ms total) 61: 61: [----------] 1 test from GmxRmsfTest 61: [ RUN ] GmxRmsfTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Select group(s) for root mean square calculation 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 61: Setting the LD random seed to 2008596406 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 3: 'C-alpha' 61: [ OK ] GmxRmsfTest.BasicOutputWorks (1480 ms) 61: [----------] 1 test from GmxRmsfTest (1480 ms total) 61: 61: [----------] 1 test from GmxSorientTest 61: [ RUN ] GmxSorientTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 1818.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Group 0 ( System) has 923 elements 61: Group 1 ( Protein) has 29 elements 61: Group 2 ( Protein-H) has 17 elements 61: Group 3 ( C-alpha) has 2 elements 61: Group 4 ( Backbone) has 6 elements 61: Group 5 ( MainChain) has 9 elements 61: Group 6 ( MainChain+Cb) has 11 elements 61: Group 7 ( MainChain+H) has 13 elements 61: Group 8 ( SideChain) has 16 elements 61: Group 9 ( SideChain-H) has 8 elements 61: Group 10 ( Prot-Masses) has 23 elements 61: Group 11 ( non-Protein) has 894 elements 61: Group 12 ( Water) has 894 elements 61: Group 13 ( SOL) has 894 elements 61: Group 14 ( non-Water) has 29 elements 61: Select a group: Select a group: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Average nr of molecules between 0 and 0.5 nm: 13.0 61: Average cos(theta1) between 0 and 0.5 nm: 0.103 61: Average 3cos2(theta2)-1 between 0 and 0.5 nm: -0.098 61: Setting the LD random seed to -100814867 61: 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.pdb', all velocities are zero 61: 61: Cleaning up constraints and constant bonded interactions with virtual sites 61: 61: Converted 15 Bonds with virtual sites to connections, 7 left 61: 61: Removed 18 Angles with virtual sites, 21 left 61: 61: Removed 10 Proper Dih.s with virtual sites, 44 left 61: Analysing residue names: 61: There are: 2 Protein residues 61: There are: 298 Water residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Select a group of reference particles and a solvent group: 61: Selected 1: 'Protein' 61: Selected 12: 'Water' 61: [ OK ] GmxSorientTest.BasicOutputWorks (77 ms) 61: [----------] 1 test from GmxSorientTest (77 ms total) 61: 61: [----------] 1 test from GmxRotmatTest 61: [ RUN ] GmxRotmatTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Setting the LD random seed to 671071989 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 4: 'Backbone' 61: [ OK ] GmxRotmatTest.BasicOutputWorks (785 ms) 61: [----------] 1 test from GmxRotmatTest (785 ms total) 61: 61: [----------] 1 test from GmxSaltbrTest 61: [ RUN ] GmxSaltbrTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 3 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 61: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: 61: Setting the LD random seed to 2138830295 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 2 Water residues 61: 61: This run will generate roughly 0 Mb of data 61: CG: SOL1-1 Q: -0.834 Atoms: 0 61: CG: SOL1-2 Q: 0.417 Atoms: 1 61: CG: SOL1-3 Q: 0.417 Atoms: 2 61: CG: SOL2-4 Q: -0.834 Atoms: 3 61: CG: SOL2-5 Q: 0.417 Atoms: 4 61: CG: SOL2-6 Q: 0.417 Atoms: 5 61: [ OK ] GmxSaltbrTest.BasicOutputWorks (44 ms) 61: [----------] 1 test from GmxSaltbrTest (44 ms total) 61: 61: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: trr version: GMX_trn_file (single precision) 61: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (2 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (4 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 61: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (11 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (3 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (4 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (7 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (3 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (4 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 61: Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (4 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (3 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (4 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (4 ms) 61: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (58 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 37 tests from 10 test suites ran. (12020 ms total) 61: [ PASSED ] 37 tests. 61/103 Test #61: GmxAnaTest ................................ Passed 12.07 sec test 62 Start 62: GmxPreprocessTests 62: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests 62: Test timeout computed to be: 1920 62: [==========] Running 282 tests from 17 test suites. 62: [----------] Global test environment set-up. 62: [----------] 1 test from ConvertInteractionsTest 62: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 62: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 62: [----------] 1 test from ConvertInteractionsTest (0 ms total) 62: 62: [----------] 5 tests from GenconfTest 62: [ RUN ] GenconfTest.nbox_Works 62: [ OK ] GenconfTest.nbox_Works (3 ms) 62: [ RUN ] GenconfTest.nbox_norenumber_Works 62: [ OK ] GenconfTest.nbox_norenumber_Works (2 ms) 62: [ RUN ] GenconfTest.nbox_dist_Works 62: [ OK ] GenconfTest.nbox_dist_Works (2 ms) 62: [ RUN ] GenconfTest.nbox_rot_Works 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 62: [ RUN ] GenconfTest.trj_Works 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Last frame 3 time 3.000 62: [ OK ] GenconfTest.trj_Works (3 ms) 62: [----------] 5 tests from GenconfTest (13 ms total) 62: 62: [----------] 2 tests from GenionTest 62: [ RUN ] GenionTest.HighConcentrationIonPlacement 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 62: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 62: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 62: on the accuracy of your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 62: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 62: buffer. The cluster pair list does have a buffering effect, but choosing 62: a larger rlist might be necessary for good energy conservation. 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 62: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 62: < 0 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 1308.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Group 0 ( System) has 653 elements 62: Group 1 ( Water) has 648 elements 62: Group 2 ( SOL) has 648 elements 62: Group 3 ( non-Water) has 5 elements 62: Group 4 ( Other) has 5 elements 62: Group 5 ( METH) has 5 elements 62: Select a group: Number of (3-atomic) solvent molecules: 216 62: Using random seed 1997. 62: Replacing solvent molecule 56 (atom 168) with NA 62: Replacing solvent molecule 120 (atom 360) with NA 62: Replacing solvent molecule 182 (atom 546) with NA 62: Replacing solvent molecule 71 (atom 213) with NA 62: Replacing solvent molecule 189 (atom 567) with CL 62: Replacing solvent molecule 54 (atom 162) with CL 62: Replacing solvent molecule 155 (atom 465) with CL 62: Replacing solvent molecule 99 (atom 297) with CL 62: 62: Setting the LD random seed to -8437825 62: 62: Generated 331705 of the 331705 non-bonded parameter combinations 62: 62: Generated 331705 of the 331705 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Excluding 3 bonded neighbours molecule type 'methane' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216_with_methane.gro' 62: Analysing residue names: 62: There are: 216 Water residues 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: This run will generate roughly 0 Mb of data 62: Will try to add 4 NA ions and 4 CL ions. 62: Select a continuous group of solvent molecules 62: Selected 1: 'Water' 62: [ OK ] GenionTest.HighConcentrationIonPlacement (866 ms) 62: [ RUN ] GenionTest.NoIonPlacement 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 62: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 62: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 62: on the accuracy of your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 62: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 62: buffer. The cluster pair list does have a buffering effect, but choosing 62: a larger rlist might be necessary for good energy conservation. 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 62: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 62: < 0 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 1308.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: No ions to add, will just copy input configuration. 62: Setting the LD random seed to -536872035 62: 62: Generated 331705 of the 331705 non-bonded parameter combinations 62: 62: Generated 331705 of the 331705 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Excluding 3 bonded neighbours molecule type 'methane' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216_with_methane.gro' 62: Analysing residue names: 62: There are: 216 Water residues 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] GenionTest.NoIonPlacement (827 ms) 62: [----------] 2 tests from GenionTest (1694 ms total) 62: 62: [----------] 1 test from GenRestrTest 62: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 62: 62: Reading structure file 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Select group to position restrain 62: Selected 3: 'C-alpha' 62: [ OK ] GenRestrTest.SimpleRestraintsGenerated (39 ms) 62: [----------] 1 test from GenRestrTest (39 ms total) 62: 62: [----------] 9 tests from PreprocessingAtomTypesTest 62: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 62: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 62: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 62: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 62: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 62: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 62: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 62: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 62: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 62: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 62: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 62: 62: [----------] 10 tests from PreprocessingBondAtomTypeTest 62: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 62: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 62: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 62: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 62: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 62: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 62: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 62: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 62: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 62: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 62: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 62: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 62: 62: [----------] 3 tests from GromppDirectiveTest 62: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -905974275 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 2111812541 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (10 ms) 62: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 62: coefficients that do not sum to zero. This does not affect the simulation 62: and can be ignored, unless you are comparing potential energy values with 62: other force field ports and/or MD software. 62: First such dihedral in molecule A, involving atoms 0 2 1 3 62: 62: 62: NOTE 2 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 3 NOTEs 62: Setting the LD random seed to -192153669 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 2143967399 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (8 ms) 62: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 62: Setting the LD random seed to -1078042665 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 1576493055 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (16 ms) 62: [----------] 3 tests from GromppDirectiveTest (35 ms total) 62: 62: [----------] 6 tests from InsertMoleculesTest 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 62: Reading solute configuration 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Try 1 success (now 8 atoms)! 62: 62: Added 1 molecules (out of 1 requested) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 62: 62: Output configuration contains 8 atoms in 4 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (5 ms) 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Try 1 success (now 2 atoms)! 62: Try 2 success (now 4 atoms)! 62: Try 3 success (now 6 atoms)! 62: Try 4 success (now 8 atoms)! 62: Try 5 success (now 10 atoms)! 62: 62: Added 5 molecules (out of 5 requested) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 62: 62: Output configuration contains 10 atoms in 10 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (3 ms) 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Try 1 success (now 2 atoms)! 62: Try 2 success (now 4 atoms)! 62: Try 3 success (now 6 atoms)! 62: Try 4 success (now 8 atoms)! 62: Try 5 success (now 10 atoms)! 62: 62: Added 5 molecules (out of 5 requested) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 62: 62: Output configuration contains 10 atoms in 10 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (3 ms) 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 62: Reading solute configuration 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Try 1 success (now 8 atoms)! 62: Try 2 success (now 10 atoms)! 62: 62: Added 2 molecules (out of 2 requested) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 62: 62: Output configuration contains 10 atoms in 4 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (5 ms) 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 62: Reading solute configuration 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Try 1 success (now 650 atoms)! 62: Try 2 success (now 652 atoms)! 62: Try 3 success (now 654 atoms)! 62: Try 4 success (now 656 atoms)! 62: 62: Added 4 molecules (out of 4 requested) 62: Replaced 8 residues (24 atoms) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 62: 62: Output configuration contains 632 atoms in 212 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (12 ms) 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Read 4 positions from file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 62: 62: Try 1 success (now 2 atoms)! 62: Try 2 success (now 4 atoms)! 62: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 62: Try 13 success (now 6 atoms)! 62: 62: Added 3 molecules (out of 4 requested) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 62: 62: Output configuration contains 6 atoms in 3 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (4 ms) 62: [----------] 6 tests from InsertMoleculesTest (34 ms total) 62: 62: [----------] 3 tests from MassRepartitioning 62: [ RUN ] MassRepartitioning.ValidCaseWorks 62: The smallest mass in the system is 2, setting the minimum mass to 6 62: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 62: [ RUN ] MassRepartitioning.UnboundGivesWarning 62: 62: WARNING 1 [file unknown]: 62: The are 1 atoms that have a mass below the mass repartitioning limit but 62: are not bound. These masses cannot be repartitioned. 62: 62: The smallest mass in the system is 2, setting the minimum mass to 6 62: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 62: [ RUN ] MassRepartitioning.LightPartnerGivesError 62: 62: ERROR 1 [file unknown]: 62: Light atoms are bound to at least one atom that has a too low mass for 62: repartitioning 62: 62: The smallest mass in the system is 2, setting the minimum mass to 6 62: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 62: [----------] 3 tests from MassRepartitioning (0 ms total) 62: 62: [----------] 36 tests from GetIrTest 62: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 62: Ignoring obsolete mdp entry 'title' 62: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (6 ms) 62: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 62: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (11 ms) 62: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsKeyWithoutValue (8 ms) 62: [ RUN ] GetIrTest.RejectsValueWithoutKey 62: [ OK ] GetIrTest.RejectsValueWithoutKey (10 ms) 62: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 62: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (10 ms) 62: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (7 ms) 62: [ RUN ] GetIrTest.AcceptsEmptyLines 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsEmptyLines (7 ms) 62: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 62: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.MtsCheckNstcalcenergy (4 ms) 62: [ RUN ] GetIrTest.MtsCheckNstenergy 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 62: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (5) 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.MtsCheckNstenergy (4 ms) 62: [ RUN ] GetIrTest.MtsCheckNstpcouple 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 62: Pressure coupling incorrect number of values (I need exactly 1) 62: 62: 62: ERROR 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 62: Pressure coupling incorrect number of values (I need exactly 1) 62: 62: 62: ERROR 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 62: With multiple time stepping, nstpcouple should be a multiple of 62: mts-factor 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: ERROR 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 62: The Berendsen barostat does not generate any strictly correct ensemble, 62: and should not be used for new production simulations (in our opinion). 62: We recommend using the C-rescale barostat instead. 62: 62: 62: ERROR 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 62: compressibility must be > 0 when using pressure coupling Berendsen 62: 62: 62: [ OK ] GetIrTest.MtsCheckNstpcouple (5 ms) 62: [ RUN ] GetIrTest.MtsCheckNstdhdl 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 62: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstdhdl (5) 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: ERROR 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 62: Lambda state must be set, either with init-lambda-state or with 62: init-lambda 62: 62: [ OK ] GetIrTest.MtsCheckNstdhdl (4 ms) 62: [ RUN ] GetIrTest.MtsCheckSDNotSupported 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 62: Multiple time stepping is only supported with integrator md 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.MtsCheckSDNotSupported (4 ms) 62: [ RUN ] GetIrTest.AcceptsElectricField 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsElectricField (6 ms) 62: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (6 ms) 62: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (6 ms) 62: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 62: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (4 ms) 62: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsImplicitSolventNo (6 ms) 62: [ RUN ] GetIrTest.RejectsImplicitSolventYes 62: [ OK ] GetIrTest.RejectsImplicitSolventYes (11 ms) 62: [ RUN ] GetIrTest.AcceptsMimic 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsMimic (8 ms) 62: [ RUN ] GetIrTest.AcceptsTransformationCoord 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 62: pull-coord2 has a non-zero force constant and is also referenced in 62: pull-coord1-expression. Make sure that this is intended. In most use 62: cases, the pull coordinates referenced by a transformation coordinate 62: should have their force constant set to zero. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsTransformationCoord (6 ms) 62: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 62: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (5 ms) 62: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 62: pull-coord2 can not use pull-coord1 in the transformation since this is a 62: constraint 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (6 ms) 62: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 62: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 62: 'transformation' 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (5 ms) 62: [ RUN ] GetIrTest.MissingTransformationCoordExpression 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 62: pull-coord1-expression not set for pull coordinate of geometry 62: 'transformation' 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.MissingTransformationCoordExpression (5 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 62: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 62: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 62: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 62: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 62: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 62: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 62: in total 100001 steps. This is not compatible with using soft-core 62: potentials. 62: 62: 62: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 62: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 62: won't change anymore after step 100000 until the end of the simulation 62: after 100001 steps. 62: 62: 62: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 62: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 62: won't change anymore after step 100000 until the end of the simulation 62: after 100001 steps. 62: 62: 62: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 62: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 62: components won't change anymore after step 100000 until the end of the 62: simulation after 100001 steps. 62: 62: 62: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 62: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 62: components won't change anymore after step 100000 until the end of the 62: simulation after 100001 steps. 62: 62: 62: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 62: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 62: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (4 ms) 62: [ RUN ] GetIrTest.AcceptsFmmOptions 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsFmmOptions_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsFmmOptions (7 ms) 62: [----------] 36 tests from GetIrTest (230 ms total) 62: 62: [----------] 6 tests from SolvateTest 62: [ RUN ] SolvateTest.cs_box_Works 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 1x1x1 boxes 62: Solvent box contains 270 atoms in 90 residues 62: Removed 129 solvent atoms due to solvent-solvent overlap 62: Sorting configuration 62: Found 1 molecule type: 62: SOL ( 3 atoms): 47 residues 62: Generated solvent containing 141 atoms in 47 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 62: 62: Output configuration contains 141 atoms in 47 residues 62: Volume : 1.331 (nm^3) 62: Density : 1056.36 (g/l) 62: Number of solvent molecules: 47 62: 62: [ OK ] SolvateTest.cs_box_Works (10 ms) 62: [ RUN ] SolvateTest.cs_cp_Works 62: Reading solute configuration 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 2x2x2 boxes 62: Solvent box contains 3660 atoms in 1220 residues 62: Removed 987 solvent atoms due to solvent-solvent overlap 62: Removed 15 solvent atoms due to solute-solvent overlap 62: Sorting configuration 62: Found 1 molecule type: 62: SOL ( 3 atoms): 886 residues 62: Generated solvent containing 2658 atoms in 886 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 62: 62: Output configuration contains 2664 atoms in 888 residues 62: Volume : 27.2709 (nm^3) 62: Density : 974.777 (g/l) 62: Number of solvent molecules: 886 62: 62: [ OK ] SolvateTest.cs_cp_Works (33 ms) 62: [ RUN ] SolvateTest.cs_cp_p_Works 62: Reading solute configuration 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 2x2x2 boxes 62: Solvent box contains 3660 atoms in 1220 residues 62: Removed 987 solvent atoms due to solvent-solvent overlap 62: Removed 15 solvent atoms due to solute-solvent overlap 62: Sorting configuration 62: Found 1 molecule type: 62: SOL ( 3 atoms): 886 residues 62: Generated solvent containing 2658 atoms in 886 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 62: 62: Output configuration contains 2664 atoms in 888 residues 62: Volume : 27.2709 (nm^3) 62: Density : 974.777 (g/l) 62: Number of solvent molecules: 886 62: 62: Processing topology 62: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 62: [ OK ] SolvateTest.cs_cp_p_Works (33 ms) 62: [ RUN ] SolvateTest.shell_Works 62: Reading solute configuration 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 2x2x2 boxes 62: Solvent box contains 3660 atoms in 1220 residues 62: Removed 987 solvent atoms due to solvent-solvent overlap 62: Removed 1902 solvent atoms more than 1.000000 nm from solute. 62: Removed 15 solvent atoms due to solute-solvent overlap 62: Sorting configuration 62: Found 1 molecule type: 62: SOL ( 3 atoms): 252 residues 62: Generated solvent containing 756 atoms in 252 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 62: 62: Output configuration contains 762 atoms in 254 residues 62: Volume : 27.2709 (nm^3) 62: Density : 279.3 (g/l) 62: Number of solvent molecules: 252 62: 62: [ OK ] SolvateTest.shell_Works (22 ms) 62: [ RUN ] SolvateTest.update_Topology_Works 62: Reading solute configuration 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 3x3x3 boxes 62: Solvent box contains 14952 atoms in 4984 residues 62: Removed 2787 solvent atoms due to solvent-solvent overlap 62: Removed 30 solvent atoms due to solute-solvent overlap 62: Sorting configuration 62: Found 2 different molecule types: 62: HOH ( 3 atoms): 1876 residues 62: SOL ( 3 atoms): 2169 residues 62: Generated solvent containing 0 atoms in 0 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 62: 62: Output configuration contains 12141 atoms in 4047 residues 62: Volume : 125 (nm^3) 62: Density : 968.963 (g/l) 62: Number of solvent molecules: 4045 62: 62: Processing topology 62: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 62: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 62: [ OK ] SolvateTest.update_Topology_Works (142 ms) 62: [ RUN ] SolvateTest.cs_pdb_big_box_Works 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 2x2x2 boxes 62: Solvent box contains 1218 atoms in 406 residues 62: Removed 555 solvent atoms due to solvent-solvent overlap 62: Sorting configuration 62: Found 1 molecule type: 62: SOL ( 3 atoms): 221 residues 62: Generated solvent containing 663 atoms in 221 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 62: 62: Output configuration contains 663 atoms in 221 residues 62: Volume : 8 (nm^3) 62: Density : 826.409 (g/l) 62: Number of solvent molecules: 221 62: 62: [ OK ] SolvateTest.cs_pdb_big_box_Works (16 ms) 62: [----------] 6 tests from SolvateTest (258 ms total) 62: 62: [----------] 1 test from TopDirTests 62: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 62: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 62: [----------] 1 test from TopDirTests (0 ms total) 62: 62: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 62: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (3 ms total) 62: 62: [----------] 45 tests from SinglePeptideFragments/EditconfTest 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (13 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (6 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (8 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (4 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (4 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (9 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (4 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (6 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 62: 62: Select a group for output: 62: Group 0 ( two_residues) has 23 elements 62: There is one group in the index 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (6 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 62: 62: Select a group for output: 62: Group 0 ( two_residues) has 23 elements 62: There is one group in the index 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 62: 62: Select a group for output: 62: Group 0 ( two_residues) has 23 elements 62: There is one group in the index 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (6 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 62: 62: Select a group for output: 62: Group 0 ( two_residues) has 23 elements 62: There is one group in the index 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (3 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 62: 62: Select a group for output: 62: Group 0 ( two_residues) has 23 elements 62: There is one group in the index 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (3 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 62: 62: Select a group for output: 62: Group 0 ( two_residues) has 23 elements 62: There is one group in the index 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (4 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 62: 62: Select a group for output: 62: Group 0 ( two_residues) has 23 elements 62: There is one group in the index 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (4 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 62: 62: Select a group for output: 62: Group 0 ( two_residues) has 23 elements 62: There is one group in the index 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (3 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 62: 62: Select a group for output: 62: Group 0 ( two_residues) has 23 elements 62: There is one group in the index 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (4 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : 0.212 1.187 3.527 (nm) 62: new center : 4.028 2.819 3.723 (nm) 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (7 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : 0.212 1.187 3.527 (nm) 62: new center : 4.028 2.819 3.723 (nm) 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (7 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : 0.212 1.187 3.527 (nm) 62: new center : 4.028 2.819 3.723 (nm) 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (6 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : 0.212 1.187 3.527 (nm) 62: new center : 4.028 2.819 3.723 (nm) 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : 0.212 1.187 3.527 (nm) 62: new center : 4.028 2.819 3.723 (nm) 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (3 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : 0.212 1.187 3.527 (nm) 62: new center : 4.028 2.819 3.723 (nm) 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (3 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : 0.212 1.187 3.527 (nm) 62: new center : 4.028 2.819 3.723 (nm) 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : 0.212 1.187 3.527 (nm) 62: new center : 4.028 2.819 3.723 (nm) 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (4 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : 0.212 1.187 3.527 (nm) 62: new center : 4.028 2.819 3.723 (nm) 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : -0.814 1.104 2.657 (nm) 62: new center : 3.002 2.736 2.852 (nm) 62: new box vectors : 6.004 5.472 5.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 187.42 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (8 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : -0.814 1.104 2.657 (nm) 62: new center : 3.002 2.736 2.852 (nm) 62: new box vectors : 6.004 5.472 5.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 187.42 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (7 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : -0.814 1.104 2.657 (nm) 62: new center : 3.002 2.736 2.852 (nm) 62: new box vectors : 6.004 5.472 5.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 187.42 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (6 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : -0.814 1.104 2.657 (nm) 62: new center : 3.002 2.736 2.852 (nm) 62: new box vectors : 6.004 5.472 5.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 187.40 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : -0.814 1.104 2.657 (nm) 62: new center : 3.002 2.736 2.852 (nm) 62: new box vectors : 6.004 5.472 5.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 187.40 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (3 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : -0.814 1.104 2.657 (nm) 62: new center : 3.002 2.736 2.852 (nm) 62: new box vectors : 6.004 5.472 5.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 187.40 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (4 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : -0.814 1.104 2.657 (nm) 62: new center : 3.002 2.736 2.852 (nm) 62: new box vectors : 6.004 5.472 5.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 187.40 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : -0.814 1.104 2.657 (nm) 62: new center : 3.002 2.736 2.852 (nm) 62: new box vectors : 6.004 5.472 5.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 187.40 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (3 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: shift : -0.814 1.104 2.657 (nm) 62: new center : 3.002 2.736 2.852 (nm) 62: new box vectors : 6.004 5.472 5.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 187.40 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: new center : 3.816 1.632 0.195 (nm) 62: new box vectors : 5.004 4.472 4.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 105.28 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (8 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: new center : 3.816 1.632 0.195 (nm) 62: new box vectors : 5.004 4.472 4.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 105.28 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (7 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: new center : 3.816 1.632 0.195 (nm) 62: new box vectors : 5.004 4.472 4.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 105.28 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (6 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: new center : 3.816 1.632 0.195 (nm) 62: new box vectors : 5.004 4.472 4.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 105.27 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (7 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: new center : 3.816 1.632 0.195 (nm) 62: new box vectors : 5.004 4.472 4.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 105.27 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (4 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: new center : 3.816 1.632 0.195 (nm) 62: new box vectors : 5.004 4.472 4.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 105.27 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: new center : 3.816 1.632 0.195 (nm) 62: new box vectors : 5.004 4.472 4.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 105.27 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: new center : 3.816 1.632 0.195 (nm) 62: new box vectors : 5.004 4.472 4.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 105.27 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (5 ms) 62: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 62: Note that major changes are planned in future for editconf, to improve usability and utility. 62: Read 252 atoms 62: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 62: No velocities found 62: system size : 2.004 1.472 1.704 (nm) 62: center : 3.816 1.632 0.195 (nm) 62: box vectors : 8.056 5.637 7.445 (nm) 62: box angles : 90.00 90.00 90.00 (degrees) 62: box volume : 338.10 (nm^3) 62: new center : 3.816 1.632 0.195 (nm) 62: new box vectors : 5.004 4.472 4.704 (nm) 62: new box angles : 90.00 90.00 90.00 (degrees) 62: new box volume : 105.27 (nm^3) 62: 62: WARNING: No boxtype specified - distance condition applied in each dimension. 62: If the molecule rotates the actual distance will be smaller. You might want 62: to use a cubic box instead, or why not try a dodecahedron today? 62: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (6 ms) 62: [----------] 45 tests from SinglePeptideFragments/EditconfTest (265 ms total) 62: 62: [----------] 16 tests from CorrectVelocity/MaxwellTest 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (2 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (2 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (2 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (2 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (3 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (4 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (3 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (4 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (4 ms) 62: [----------] 16 tests from CorrectVelocity/MaxwellTest (43 ms total) 62: 62: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -453115971 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -234930817 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -1344392323 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -851452049 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -109445933 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -675283459 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to 1852305885 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1352945921 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to 2077079736 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -637741098 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to 2042623738 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -637551617 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -79995977 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -186980641 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -6326817 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -444663825 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to 1876942831 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -134285569 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to 1845457401 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -8493059 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to 1870626758 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -1476704410 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -1627656709 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -100796705 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -1075843149 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -715221009 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to 1070135285 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -543686745 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -105488563 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to 2080369613 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -811944969 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -1092665473 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -4194348 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -134295729 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -50333185 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1151352833 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 (8 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 62: Setting the LD random seed to -1344929829 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -1356880257 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 (8 ms) 62: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest (168 ms total) 62: 62: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 62: Setting the LD random seed to -1142952217 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (15 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 62: Setting the LD random seed to 2038291189 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (12 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to 1608720373 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1125253637 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (9 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -30543873 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 1593175287 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (8 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -11280386 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -541103929 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (8 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -1673597969 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -43515925 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (8 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 62: Setting the LD random seed to -1138960 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 62: Setting the LD random seed to 2144960475 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -285475185 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (14 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 62: Setting the LD random seed to -8454145 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (12 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 62: Setting the LD random seed to -106006534 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1293977738 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 62: Setting the LD random seed to -1946715395 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 2129063902 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 62: Setting the LD random seed to -14788801 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1704279 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (14 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 62: Setting the LD random seed to -570505217 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1312129 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 62: Setting the LD random seed to -42225736 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 2061496315 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 62: Setting the LD random seed to 2011168495 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -68175882 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (14 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 62: Setting the LD random seed to 2145123433 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 2147407812 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (14 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -244561025 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 1338376101 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (8 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -56904267 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 834627183 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (8 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 62: Setting the LD random seed to -541336884 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 62: Setting the LD random seed to -94376001 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -285738017 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (14 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 62: Setting the LD random seed to -243569313 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -158141441 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1213899337 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (8 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 62: Setting the LD random seed to 1979569147 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 62: Setting the LD random seed to -1612709937 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -405405713 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 (13 ms) 62: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest (298 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 282 tests from 17 test suites ran. (3086 ms total) 62: [ PASSED ] 242 tests. 62: [ SKIPPED ] 40 tests, listed below: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 62/103 Test #62: GmxPreprocessTests ........................ Passed 3.13 sec test 63 Start 63: Pdb2gmx1Test 63: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 63: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests 63: Test timeout computed to be: 1920 63: [==========] Running 30 tests from 1 test suite. 63: [----------] Global test environment set-up. 63: [----------] 30 tests from Oplsaa/Pdb2gmxTest 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 0 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (62 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 0 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (64 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 0 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (58 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 0 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (54 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 0 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (165 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Marked 124 virtual sites 63: Added 16 dummy masses 63: Added 26 new constraints 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 130 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (63 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Marked 132 virtual sites 63: Added 10 dummy masses 63: Added 19 new constraints 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 133 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (67 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Marked 123 virtual sites 63: Added 22 dummy masses 63: Added 35 new constraints 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 132 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (65 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Marked 111 virtual sites 63: Added 18 dummy masses 63: Added 31 new constraints 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 116 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (60 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Marked 447 virtual sites 63: Added 58 dummy masses 63: Added 101 new constraints 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 462 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (188 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 0 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (59 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 0 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (63 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 0 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (58 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 0 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (53 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 0 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (163 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Marked 124 virtual sites 63: Added 16 dummy masses 63: Added 26 new constraints 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 130 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (64 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Marked 132 virtual sites 63: Added 10 dummy masses 63: Added 19 new constraints 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 133 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (68 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Marked 123 virtual sites 63: Added 22 dummy masses 63: Added 35 new constraints 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 132 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (66 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Marked 111 virtual sites 63: Added 18 dummy masses 63: Added 31 new constraints 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 116 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (58 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Marked 447 virtual sites 63: Added 58 dummy masses 63: Added 101 new constraints 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 462 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (187 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 0 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (58 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 0 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (64 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 0 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (57 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 0 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (53 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 0 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (163 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Marked 124 virtual sites 63: Added 16 dummy masses 63: Added 26 new constraints 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 130 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (63 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Marked 132 virtual sites 63: Added 10 dummy masses 63: Added 19 new constraints 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 133 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (69 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Marked 123 virtual sites 63: Added 22 dummy masses 63: Added 35 new constraints 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 132 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (65 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Marked 111 virtual sites 63: Added 18 dummy masses 63: Added 31 new constraints 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 116 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge -0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (59 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Marked 447 virtual sites 63: Added 58 dummy masses 63: Added 101 new constraints 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 462 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (186 ms) 63: [----------] 30 tests from Oplsaa/Pdb2gmxTest (2538 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 30 tests from 1 test suite ran. (2538 ms total) 63: [ PASSED ] 30 tests. 63/103 Test #63: Pdb2gmx1Test .............................. Passed 2.57 sec test 64 Start 64: Pdb2gmx2Test 64: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 64: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests 64: Test timeout computed to be: 1920 64: [==========] Running 40 tests from 2 test suites. 64: [----------] Global test environment set-up. 64: [----------] 20 tests from G43a1/Pdb2gmxTest 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 305 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 165 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 172, now 167 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 77 impropers, 241 angles 64: 267 pairs, 167 bonds and 0 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (80 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 429 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 202 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 216, now 211 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 134 impropers, 316 angles 64: 273 pairs, 211 bonds and 0 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (77 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 349 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 168 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 179, now 174 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 102 impropers, 260 angles 64: 242 pairs, 174 bonds and 0 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (74 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 299 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 150 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 159, now 154 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 80 impropers, 227 angles 64: 232 pairs, 154 bonds and 0 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (68 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1256 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 635 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 655, now 650 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 350 impropers, 955 angles 64: 972 pairs, 650 bonds and 0 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (140 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 37 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 305 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 165 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 172, now 167 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 77 impropers, 241 angles 64: 267 pairs, 167 bonds and 37 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (75 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 53 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 429 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 202 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 216, now 211 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 134 impropers, 316 angles 64: 273 pairs, 211 bonds and 51 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (80 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 36 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 349 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 168 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 179, now 174 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 102 impropers, 260 angles 64: 242 pairs, 174 bonds and 36 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (74 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 33 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 299 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 150 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 159, now 154 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 80 impropers, 227 angles 64: 232 pairs, 154 bonds and 31 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (71 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 146 virtual sites 64: Added 10 dummy masses 64: Added 29 new constraints 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1256 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 635 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 655, now 650 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 350 impropers, 955 angles 64: 972 pairs, 650 bonds and 137 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (147 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 305 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 165 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 172, now 167 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 77 impropers, 241 angles 64: 267 pairs, 167 bonds and 0 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (114 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 429 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 202 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 216, now 211 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 134 impropers, 316 angles 64: 273 pairs, 211 bonds and 0 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (75 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 349 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 168 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 179, now 174 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 102 impropers, 260 angles 64: 242 pairs, 174 bonds and 0 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (73 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 299 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 150 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 159, now 154 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 80 impropers, 227 angles 64: 232 pairs, 154 bonds and 0 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (68 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1256 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 635 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 655, now 650 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 350 impropers, 955 angles 64: 972 pairs, 650 bonds and 0 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (137 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 37 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 305 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 165 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 172, now 167 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 77 impropers, 241 angles 64: 267 pairs, 167 bonds and 37 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (74 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 53 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 429 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 202 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 216, now 211 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 134 impropers, 316 angles 64: 273 pairs, 211 bonds and 51 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (87 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 36 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 349 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 168 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 179, now 174 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 102 impropers, 260 angles 64: 242 pairs, 174 bonds and 36 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (75 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 33 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 299 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 150 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 159, now 154 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 80 impropers, 227 angles 64: 232 pairs, 154 bonds and 31 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (72 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 146 virtual sites 64: Added 10 dummy masses 64: Added 29 new constraints 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1256 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 635 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 655, now 650 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 350 impropers, 955 angles 64: 972 pairs, 650 bonds and 137 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (145 ms) 64: [----------] 20 tests from G43a1/Pdb2gmxTest (1816 ms total) 64: 64: [----------] 20 tests from G53a6/Pdb2gmxTest 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 312 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 167 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 174, now 169 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 79 impropers, 245 angles 64: 267 pairs, 169 bonds and 0 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (124 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 443 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 206 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 220, now 215 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 138 impropers, 324 angles 64: 273 pairs, 215 bonds and 0 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (84 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 356 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 170 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 181, now 176 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 104 impropers, 264 angles 64: 242 pairs, 176 bonds and 0 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (82 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 306 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 152 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 161, now 156 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 82 impropers, 231 angles 64: 232 pairs, 156 bonds and 0 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (77 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1270 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 639 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 659, now 654 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 354 impropers, 963 angles 64: 972 pairs, 654 bonds and 0 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (145 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 39 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 312 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 167 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 174, now 169 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 79 impropers, 245 angles 64: 267 pairs, 169 bonds and 39 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (82 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 57 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 443 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 206 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 220, now 215 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 138 impropers, 324 angles 64: 273 pairs, 215 bonds and 55 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (88 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 38 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 356 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 170 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 181, now 176 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 104 impropers, 264 angles 64: 242 pairs, 176 bonds and 38 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (82 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 35 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 306 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 152 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 161, now 156 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 82 impropers, 231 angles 64: 232 pairs, 156 bonds and 33 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (84 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 150 virtual sites 64: Added 10 dummy masses 64: Added 29 new constraints 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1270 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 639 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 659, now 654 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 354 impropers, 963 angles 64: 972 pairs, 654 bonds and 141 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (153 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 312 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 167 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 174, now 169 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 79 impropers, 245 angles 64: 267 pairs, 169 bonds and 0 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (113 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 443 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 206 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 220, now 215 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 138 impropers, 324 angles 64: 273 pairs, 215 bonds and 0 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (84 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 356 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 170 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 181, now 176 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 104 impropers, 264 angles 64: 242 pairs, 176 bonds and 0 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (79 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 306 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 152 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 161, now 156 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 82 impropers, 231 angles 64: 232 pairs, 156 bonds and 0 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (75 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1270 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 639 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 659, now 654 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 354 impropers, 963 angles 64: 972 pairs, 654 bonds and 0 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (150 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 39 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 312 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 167 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 174, now 169 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 79 impropers, 245 angles 64: 267 pairs, 169 bonds and 39 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (125 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 57 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 443 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 206 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 220, now 215 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 138 impropers, 324 angles 64: 273 pairs, 215 bonds and 55 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (87 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 38 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 356 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 170 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 181, now 176 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 104 impropers, 264 angles 64: 242 pairs, 176 bonds and 38 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (82 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 35 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 306 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 152 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 161, now 156 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 82 impropers, 231 angles 64: 232 pairs, 156 bonds and 33 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (83 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 150 virtual sites 64: Added 10 dummy masses 64: Added 29 new constraints 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1270 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 639 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 659, now 654 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 354 impropers, 963 angles 64: 972 pairs, 654 bonds and 141 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (158 ms) 64: [----------] 20 tests from G53a6/Pdb2gmxTest (2050 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 40 tests from 2 test suites ran. (3868 ms total) 64: [ PASSED ] 40 tests. 64/103 Test #64: Pdb2gmx2Test .............................. Passed 3.90 sec test 65 Start 65: Pdb2gmx3Test 65: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 65: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/gmxpreprocess/tests 65: Test timeout computed to be: 1920 65: [==========] Running 55 tests from 9 test suites. 65: [----------] Global test environment set-up. 65: [----------] 10 tests from Amber/Pdb2gmxTest 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Before cleaning: 653 pairs 65: Before cleaning: 691 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 255, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 691 dihedrals, 51 impropers, 457 angles 65: 650 pairs, 254 bonds and 0 virtual sites 65: 65: Total mass 1846.132 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (92 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Before cleaning: 748 pairs 65: Before cleaning: 788 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 291, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 788 dihedrals, 72 impropers, 516 angles 65: 736 pairs, 290 bonds and 0 virtual sites 65: 65: Total mass 2088.366 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (88 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Before cleaning: 676 pairs 65: Before cleaning: 727 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 262, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 727 dihedrals, 56 impropers, 472 angles 65: 667 pairs, 261 bonds and 0 virtual sites 65: 65: Total mass 1861.124 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (85 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Before cleaning: 603 pairs 65: Before cleaning: 634 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 233, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 634 dihedrals, 48 impropers, 419 angles 65: 597 pairs, 232 bonds and 0 virtual sites 65: 65: Total mass 1662.888 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (79 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Before cleaning: 2499 pairs 65: Before cleaning: 2631 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 952, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2631 dihedrals, 208 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 0 virtual sites 65: 65: Total mass 6908.576 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (205 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Marked 124 virtual sites 65: Added 16 dummy masses 65: Added 26 new constraints 65: Before cleaning: 653 pairs 65: Before cleaning: 691 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 255, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 691 dihedrals, 51 impropers, 457 angles 65: 650 pairs, 254 bonds and 130 virtual sites 65: 65: Total mass 1846.132 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (88 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Marked 132 virtual sites 65: Added 10 dummy masses 65: Added 19 new constraints 65: Before cleaning: 748 pairs 65: Before cleaning: 788 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 291, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 788 dihedrals, 72 impropers, 516 angles 65: 736 pairs, 290 bonds and 133 virtual sites 65: 65: Total mass 2088.366 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (99 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Marked 123 virtual sites 65: Added 22 dummy masses 65: Added 35 new constraints 65: Before cleaning: 676 pairs 65: Before cleaning: 727 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 262, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 727 dihedrals, 56 impropers, 472 angles 65: 667 pairs, 261 bonds and 132 virtual sites 65: 65: Total mass 1861.124 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (88 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Marked 111 virtual sites 65: Added 18 dummy masses 65: Added 31 new constraints 65: Before cleaning: 603 pairs 65: Before cleaning: 634 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 233, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 634 dihedrals, 48 impropers, 419 angles 65: 597 pairs, 232 bonds and 116 virtual sites 65: 65: Total mass 1662.888 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (84 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Marked 447 virtual sites 65: Added 58 dummy masses 65: Added 101 new constraints 65: Before cleaning: 2499 pairs 65: Before cleaning: 2631 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 952, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2631 dihedrals, 208 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 462 virtual sites 65: 65: Total mass 6908.576 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (228 ms) 65: [----------] 10 tests from Amber/Pdb2gmxTest (1145 ms total) 65: 65: [----------] 1 test from AmberTip4p/Pdb2gmxTest 65: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 65: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 2 4 (only water) 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (4 atoms, 2 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 2 residues with 8 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 4, now 4 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 2 angles 65: 0 pairs, 4 bonds and 0 virtual sites 65: 65: Total mass 36.032 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 65: 65: The Amber99sb-ildn force field and the tip4p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (41 ms) 65: [----------] 1 test from AmberTip4p/Pdb2gmxTest (42 ms total) 65: 65: [----------] 10 tests from Amber14Sb/Pdb2gmxTest 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Before cleaning: 653 pairs 65: Before cleaning: 663 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 254, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 663 dihedrals, 51 impropers, 457 angles 65: 650 pairs, 254 bonds and 0 virtual sites 65: 65: Total mass 1846.132 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Amber14sb force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (68 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Before cleaning: 748 pairs 65: Before cleaning: 778 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 290, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 778 dihedrals, 76 impropers, 516 angles 65: 736 pairs, 290 bonds and 0 virtual sites 65: 65: Total mass 2088.366 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Amber14sb force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (68 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Before cleaning: 676 pairs 65: Before cleaning: 696 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 261, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 696 dihedrals, 58 impropers, 472 angles 65: 667 pairs, 261 bonds and 0 virtual sites 65: 65: Total mass 1861.124 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Amber14sb force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Before cleaning: 603 pairs 65: Before cleaning: 618 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 232, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 618 dihedrals, 48 impropers, 419 angles 65: 597 pairs, 232 bonds and 0 virtual sites 65: 65: Total mass 1662.888 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Amber14sb force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (61 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Before cleaning: 2499 pairs 65: Before cleaning: 2524 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 951, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2524 dihedrals, 210 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 0 virtual sites 65: 65: Total mass 6908.576 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Amber14sb force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (172 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Before cleaning: 653 pairs 65: Before cleaning: 663 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 254, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 663 dihedrals, 51 impropers, 457 angles 65: 650 pairs, 254 bonds and 0 virtual sites 65: 65: Total mass 1846.132 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Amber14sb force field and the opc3 water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (79 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Before cleaning: 748 pairs 65: Before cleaning: 778 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 290, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 778 dihedrals, 76 impropers, 516 angles 65: 736 pairs, 290 bonds and 0 virtual sites 65: 65: Total mass 2088.366 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Amber14sb force field and the opc3 water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (70 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Before cleaning: 676 pairs 65: Before cleaning: 696 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 261, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 696 dihedrals, 58 impropers, 472 angles 65: 667 pairs, 261 bonds and 0 virtual sites 65: 65: Total mass 1861.124 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Amber14sb force field and the opc3 water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Before cleaning: 603 pairs 65: Before cleaning: 618 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 232, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 618 dihedrals, 48 impropers, 419 angles 65: 597 pairs, 232 bonds and 0 virtual sites 65: 65: Total mass 1662.888 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Amber14sb force field and the opc3 water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (65 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Before cleaning: 2499 pairs 65: Before cleaning: 2524 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 951, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2524 dihedrals, 210 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 0 virtual sites 65: 65: Total mass 6908.576 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Amber14sb force field and the opc3 water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (172 ms) 65: [----------] 10 tests from Amber14Sb/Pdb2gmxTest (891 ms total) 65: 65: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest 65: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Using the Amber19sb force field in directory amber19sb.ff 65: 65: going to rename amber19sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 65: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 2 4 (only water) 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber19sb) 65: 65: Processing chain 1 (4 atoms, 2 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 2 residues with 8 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 4, now 4 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 2 angles 65: 0 pairs, 4 bonds and 0 virtual sites 65: 65: Total mass 36.032 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 65: 65: The Amber19sb force field and the opc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (54 ms) 65: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Using the Amber19sb force field in directory amber19sb.ff 65: 65: going to rename amber19sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 65: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 2 4 (only water) 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber19sb) 65: 65: Processing chain 1 (4 atoms, 2 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 2 residues with 8 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 4, now 4 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 2 angles 65: 0 pairs, 4 bonds and 0 virtual sites 65: 65: Total mass 36.032 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 65: 65: The Amber19sb force field and the tip4pew water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (28 ms) 65: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest (83 ms total) 65: 65: [----------] 12 tests from Charmm/Pdb2gmxTest 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 653 pairs 65: Before cleaning: 663 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 254, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 663 dihedrals, 48 impropers, 457 angles 65: 650 pairs, 254 bonds and 0 virtual sites 65: 65: Total mass 1846.115 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (88 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 748 pairs 65: Before cleaning: 778 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 290, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 778 dihedrals, 49 impropers, 516 angles 65: 736 pairs, 290 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (83 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 676 pairs 65: Before cleaning: 696 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 261, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 696 dihedrals, 39 impropers, 472 angles 65: 667 pairs, 261 bonds and 0 virtual sites 65: 65: Total mass 1861.130 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (77 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 603 pairs 65: Before cleaning: 618 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 232, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 618 dihedrals, 38 impropers, 419 angles 65: 597 pairs, 232 bonds and 0 virtual sites 65: 65: Total mass 1662.885 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (72 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 2499 pairs 65: Before cleaning: 2524 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 951, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 56 cmap torsion pairs 65: 65: There are 2524 dihedrals, 149 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 0 virtual sites 65: 65: Total mass 6908.566 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (191 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 39 pairs 65: Before cleaning: 39 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/monomer.pdb... 65: Read 'GLU', 9 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 65: 65: chain #res #atoms 65: 65: 1 'X' 1 9 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'X' (9 atoms, 1 residues) 65: 65: Identified residue GLU1 as a starting terminus. 65: 65: Identified residue GLU1 as a ending terminus. 65: Start terminus GLU-1: NH3+ 65: End terminus GLU-1: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 1 residues with 18 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 17, now 17 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 39 dihedrals, 2 impropers, 30 angles 65: 39 pairs, 17 bonds and 0 virtual sites 65: 65: Total mass 146.123 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/monomer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (44 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 124 virtual sites 65: Added 16 dummy masses 65: Added 26 new constraints 65: Before cleaning: 653 pairs 65: Before cleaning: 663 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 254, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 663 dihedrals, 48 impropers, 457 angles 65: 650 pairs, 254 bonds and 130 virtual sites 65: 65: Total mass 1846.115 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (84 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 132 virtual sites 65: Added 10 dummy masses 65: Added 19 new constraints 65: Before cleaning: 748 pairs 65: Before cleaning: 778 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 290, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 778 dihedrals, 49 impropers, 516 angles 65: 736 pairs, 290 bonds and 133 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (88 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 123 virtual sites 65: Added 22 dummy masses 65: Added 35 new constraints 65: Before cleaning: 676 pairs 65: Before cleaning: 696 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 261, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 696 dihedrals, 39 impropers, 472 angles 65: 667 pairs, 261 bonds and 132 virtual sites 65: 65: Total mass 1861.130 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (80 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 111 virtual sites 65: Added 18 dummy masses 65: Added 31 new constraints 65: Before cleaning: 603 pairs 65: Before cleaning: 618 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 232, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 618 dihedrals, 38 impropers, 419 angles 65: 597 pairs, 232 bonds and 116 virtual sites 65: 65: Total mass 1662.885 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (76 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 447 virtual sites 65: Added 58 dummy masses 65: Added 101 new constraints 65: Before cleaning: 2499 pairs 65: Before cleaning: 2524 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 951, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 56 cmap torsion pairs 65: 65: There are 2524 dihedrals, 149 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 462 virtual sites 65: 65: Total mass 6908.566 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (203 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 8 virtual sites 65: Added 2 dummy masses 65: Added 3 new constraints 65: Before cleaning: 39 pairs 65: Before cleaning: 39 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/monomer.pdb... 65: Read 'GLU', 9 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 65: 65: chain #res #atoms 65: 65: 1 'X' 1 9 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'X' (9 atoms, 1 residues) 65: 65: Identified residue GLU1 as a starting terminus. 65: 65: Identified residue GLU1 as a ending terminus. 65: Start terminus GLU-1: NH3+ 65: End terminus GLU-1: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 1 residues with 18 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 17, now 17 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 39 dihedrals, 2 impropers, 30 angles 65: 39 pairs, 17 bonds and 9 virtual sites 65: 65: Total mass 146.123 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/monomer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (45 ms) 65: [----------] 12 tests from Charmm/Pdb2gmxTest (1137 ms total) 65: 65: [----------] 8 tests from ChainSep/Pdb2gmxTest 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 651 pairs 65: Before cleaning: 661 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on changing chain id only (ignoring TER records). 65: 65: Merged chains into joint molecule definitions at 2 places. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 16 127 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (127 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue GLU5 as a ending terminus. 65: 65: Identified residue PHE6 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus GLU-5: COO- 65: Start terminus PHE-6: NH3+ 65: End terminus MET-12: COO- 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 258 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 258, now 258 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 10 cmap torsion pairs 65: 65: There are 661 dihedrals, 46 impropers, 463 angles 65: 648 pairs, 258 bonds and 0 virtual sites 65: 65: Total mass 1882.146 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (76 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 123 pairs 65: Before cleaning: 123 dihedrals 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 10 donors and 7 acceptors were found. 65: There are 7 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS8 65: NE223 65: MET12 SD55 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 317 pairs 65: Before cleaning: 322 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 211 pairs 65: Before cleaning: 216 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on changing chain id only (ignoring TER records). 65: 65: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 4 28 65: 65: 2 'B' 7 58 65: 65: 3 'C' 5 41 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (28 atoms, 4 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue GLU5 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus GLU-5: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 4 residues with 51 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 50, now 50 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2 cmap torsion pairs 65: 65: There are 123 dihedrals, 9 impropers, 88 angles 65: 123 pairs, 50 bonds and 0 virtual sites 65: 65: Total mass 434.421 a.m.u. 65: 65: Total charge -2.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (58 atoms, 7 residues) 65: 65: Identified residue PHE6 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: Start terminus PHE-6: NH3+ 65: End terminus MET-12: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 7 residues with 124 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 125, now 125 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 5 cmap torsion pairs 65: 65: There are 322 dihedrals, 19 impropers, 227 angles 65: 314 pairs, 125 bonds and 0 virtual sites 65: 65: Total mass 846.083 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Processing chain 3 'C' (41 atoms, 5 residues) 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 83 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 83, now 83 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 3 cmap torsion pairs 65: 65: There are 216 dihedrals, 18 impropers, 148 angles 65: 211 pairs, 83 bonds and 0 virtual sites 65: 65: Total mass 601.643 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 51 atoms 4 residues 65: 65: Including chain 2 in system: 124 atoms 7 residues 65: 65: Including chain 3 in system: 83 atoms 5 residues 65: 65: Now there are 258 atoms and 16 residues 65: 65: Total mass in system 1882.146 a.m.u. 65: 65: Total charge in system 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (64 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 651 pairs 65: Before cleaning: 661 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records only (ignoring chain id). 65: 65: Merged chains into joint molecule definitions at 2 places. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 16 127 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (127 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ILE9 as a ending terminus. 65: 65: Identified residue LYS10 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ILE-9: COO- 65: Start terminus LYS-10: NH3+ 65: End terminus MET-12: COO- 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 258 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 258, now 258 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 10 cmap torsion pairs 65: 65: There are 661 dihedrals, 46 impropers, 463 angles 65: 648 pairs, 258 bonds and 0 virtual sites 65: 65: Total mass 1882.146 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (76 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 10 donors and 12 acceptors were found. 65: There are 13 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 65: SG9 65: HIS8 NE251 1.055 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 288 pairs 65: Before cleaning: 293 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 152 pairs 65: Before cleaning: 152 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 211 pairs 65: Before cleaning: 216 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records only (ignoring chain id). 65: 65: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 8 61 65: 65: 2 'B' 3 25 65: 65: 3 'C' 5 41 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (61 atoms, 8 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ILE9 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ILE-9: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 8 residues with 114 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 115, now 115 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 6 cmap torsion pairs 65: 65: There are 293 dihedrals, 23 impropers, 203 angles 65: 285 pairs, 115 bonds and 0 virtual sites 65: 65: Total mass 888.952 a.m.u. 65: 65: Total charge -2.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (25 atoms, 3 residues) 65: 65: Identified residue LYS10 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: Start terminus LYS-10: NH3+ 65: End terminus MET-12: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 61 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 60, now 60 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 152 dihedrals, 5 impropers, 112 angles 65: 152 pairs, 60 bonds and 0 virtual sites 65: 65: Total mass 391.552 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Processing chain 3 'C' (41 atoms, 5 residues) 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 83 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 83, now 83 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 3 cmap torsion pairs 65: 65: There are 216 dihedrals, 18 impropers, 148 angles 65: 211 pairs, 83 bonds and 0 virtual sites 65: 65: Total mass 601.643 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 114 atoms 8 residues 65: 65: Including chain 2 in system: 61 atoms 3 residues 65: 65: Including chain 3 in system: 83 atoms 5 residues 65: 65: Now there are 258 atoms and 16 residues 65: 65: Total mass in system 1882.146 a.m.u. 65: 65: Total charge in system 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (64 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 650 pairs 65: Before cleaning: 660 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Merged chains into joint molecule definitions at 3 places. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 16 127 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (127 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue GLU5 as a ending terminus. 65: 65: Identified residue PHE6 as a starting terminus. 65: 65: Identified residue ILE9 as a ending terminus. 65: 65: Identified residue LYS10 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus GLU-5: COO- 65: Start terminus PHE-6: NH3+ 65: End terminus ILE-9: COO- 65: Start terminus LYS-10: NH3+ 65: End terminus MET-12: COO- 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 261 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 260, now 260 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 8 cmap torsion pairs 65: 65: There are 660 dihedrals, 45 impropers, 466 angles 65: 647 pairs, 260 bonds and 0 virtual sites 65: 65: Total mass 1900.162 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (78 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 65: 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 123 pairs 65: Before cleaning: 123 dihedrals 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 6 donors and 4 acceptors were found. 65: There are 3 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 164 pairs 65: Before cleaning: 169 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 152 pairs 65: Before cleaning: 152 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 211 pairs 65: Before cleaning: 216 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 65: 65: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 4 28 65: 65: 2 'B' 4 33 65: 65: 3 'B' 3 25 65: 65: 4 'C' 5 41 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (28 atoms, 4 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue GLU5 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus GLU-5: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 4 residues with 51 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 50, now 50 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2 cmap torsion pairs 65: 65: There are 123 dihedrals, 9 impropers, 88 angles 65: 123 pairs, 50 bonds and 0 virtual sites 65: 65: Total mass 434.421 a.m.u. 65: 65: Total charge -2.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (33 atoms, 4 residues) 65: 65: Identified residue PHE6 as a starting terminus. 65: 65: Identified residue ILE9 as a ending terminus. 65: Start terminus PHE-6: NH3+ 65: End terminus ILE-9: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 4 residues with 66 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 67, now 67 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2 cmap torsion pairs 65: 65: There are 169 dihedrals, 13 impropers, 118 angles 65: 161 pairs, 67 bonds and 0 virtual sites 65: 65: Total mass 472.547 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Processing chain 3 'B' (25 atoms, 3 residues) 65: 65: Identified residue LYS10 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: Start terminus LYS-10: NH3+ 65: End terminus MET-12: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 61 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 60, now 60 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 152 dihedrals, 5 impropers, 112 angles 65: 152 pairs, 60 bonds and 0 virtual sites 65: 65: Total mass 391.552 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Processing chain 4 'C' (41 atoms, 5 residues) 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 83 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 83, now 83 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 3 cmap torsion pairs 65: 65: There are 216 dihedrals, 18 impropers, 148 angles 65: 211 pairs, 83 bonds and 0 virtual sites 65: 65: Total mass 601.643 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 51 atoms 4 residues 65: 65: Including chain 2 in system: 66 atoms 4 residues 65: 65: Including chain 3 in system: 61 atoms 3 residues 65: 65: Including chain 4 in system: 83 atoms 5 residues 65: 65: Now there are 261 atoms and 16 residues 65: 65: Total mass in system 1900.162 a.m.u. 65: 65: Total charge in system 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (67 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 652 pairs 65: Before cleaning: 662 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records and chain id changing. 65: 65: Merged chains into joint molecule definitions at 1 places. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 16 127 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (127 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus MET-12: COO- 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 256, now 256 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 12 cmap torsion pairs 65: 65: There are 662 dihedrals, 47 impropers, 460 angles 65: 649 pairs, 256 bonds and 0 virtual sites 65: 65: Total mass 1864.131 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (76 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 14 donors and 15 acceptors were found. 65: There are 20 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 441 pairs 65: Before cleaning: 446 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 211 pairs 65: Before cleaning: 216 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records and chain id changing. 65: 65: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 11 86 65: 65: 2 'C' 5 41 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (86 atoms, 11 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus MET-12: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 11 residues with 172 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 173, now 173 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 9 cmap torsion pairs 65: 65: There are 446 dihedrals, 29 impropers, 312 angles 65: 438 pairs, 173 bonds and 0 virtual sites 65: 65: Total mass 1262.488 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'C' (41 atoms, 5 residues) 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 83 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 83, now 83 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 3 cmap torsion pairs 65: 65: There are 216 dihedrals, 18 impropers, 148 angles 65: 211 pairs, 83 bonds and 0 virtual sites 65: 65: Total mass 601.643 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 172 atoms 11 residues 65: 65: Including chain 2 in system: 83 atoms 5 residues 65: 65: Now there are 255 atoms and 16 residues 65: 65: Total mass in system 1864.131 a.m.u. 65: 65: Total charge in system 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (62 ms) 65: [----------] 8 tests from ChainSep/Pdb2gmxTest (568 ms total) 65: 65: [----------] 4 tests from ChainChanges/Pdb2gmxTest 65: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 83 pairs 65: Before cleaning: 83 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 145 pairs 65: Before cleaning: 150 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb... 65: Read 'Fragments of peptides and ions', 47 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on changing chain id only (ignoring TER records). 65: 65: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 3 19 65: 65: 2 'B' 3 28 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (19 atoms, 3 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ASP4 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ASP-4: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 36 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 35, now 35 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 83 dihedrals, 6 impropers, 61 angles 65: 83 pairs, 35 bonds and 0 virtual sites 65: 65: Total mass 306.314 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (28 atoms, 3 residues) 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue TRP20 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus TRP-20: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 57 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 58, now 58 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 150 dihedrals, 5 impropers, 103 angles 65: 142 pairs, 58 bonds and 0 virtual sites 65: 65: Total mass 404.468 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 36 atoms 3 residues 65: 65: Including chain 2 in system: 57 atoms 3 residues 65: 65: Now there are 93 atoms and 6 residues 65: 65: Total mass in system 710.782 a.m.u. 65: 65: Total charge in system -1.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (48 ms) 65: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 83 pairs 65: Before cleaning: 83 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 145 pairs 65: Before cleaning: 150 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb... 65: Read 'Fragments of peptides and ions', 47 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records only (ignoring chain id). 65: 65: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 3 19 65: 65: 2 'B' 3 28 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (19 atoms, 3 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ASP4 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ASP-4: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 36 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 35, now 35 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 83 dihedrals, 6 impropers, 61 angles 65: 83 pairs, 35 bonds and 0 virtual sites 65: 65: Total mass 306.314 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (28 atoms, 3 residues) 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue TRP20 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus TRP-20: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 57 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 58, now 58 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 150 dihedrals, 5 impropers, 103 angles 65: 142 pairs, 58 bonds and 0 virtual sites 65: 65: Total mass 404.468 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 36 atoms 3 residues 65: 65: Including chain 2 in system: 57 atoms 3 residues 65: 65: Now there are 93 atoms and 6 residues 65: 65: Total mass in system 710.782 a.m.u. 65: 65: Total charge in system -1.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (48 ms) 65: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 83 pairs 65: Before cleaning: 83 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 145 pairs 65: Before cleaning: 150 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb... 65: Read 'Fragments of peptides and ions', 47 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 3 19 65: 65: 2 'B' 3 28 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (19 atoms, 3 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ASP4 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ASP-4: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 36 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 35, now 35 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 83 dihedrals, 6 impropers, 61 angles 65: 83 pairs, 35 bonds and 0 virtual sites 65: 65: Total mass 306.314 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (28 atoms, 3 residues) 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue TRP20 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus TRP-20: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 57 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 58, now 58 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 150 dihedrals, 5 impropers, 103 angles 65: 142 pairs, 58 bonds and 0 virtual sites 65: 65: Total mass 404.468 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 36 atoms 3 residues 65: 65: Including chain 2 in system: 57 atoms 3 residues 65: 65: Now there are 93 atoms and 6 residues 65: 65: Total mass in system 710.782 a.m.u. 65: 65: Total charge in system -1.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (48 ms) 65: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 83 pairs 65: Before cleaning: 83 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 145 pairs 65: Before cleaning: 150 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb... 65: Read 'Fragments of peptides and ions', 47 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records and chain id changing. 65: 65: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 3 19 65: 65: 2 'B' 3 28 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (19 atoms, 3 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ASP4 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ASP-4: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 36 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 35, now 35 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 83 dihedrals, 6 impropers, 61 angles 65: 83 pairs, 35 bonds and 0 virtual sites 65: 65: Total mass 306.314 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (28 atoms, 3 residues) 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue TRP20 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus TRP-20: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 57 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 58, now 58 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 150 dihedrals, 5 impropers, 103 angles 65: 142 pairs, 58 bonds and 0 virtual sites 65: 65: Total mass 404.468 a.m.u. 65: 65: Total charge -0.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 36 atoms 3 residues 65: 65: Including chain 2 in system: 57 atoms 3 residues 65: 65: Now there are 93 atoms and 6 residues 65: 65: Total mass in system 710.782 a.m.u. 65: 65: Total charge in system -1.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (48 ms) 65: [----------] 4 tests from ChainChanges/Pdb2gmxTest (193 ms total) 65: 65: [----------] 4 tests from Cyclic/Pdb2gmxTest 65: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: WARNING: all CONECT records are ignored 65: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 65: 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 6040 pairs 65: Before cleaning: 6605 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 6040 pairs 65: Before cleaning: 6605 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 65: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 65: 65: Moved all the water blocks to the end 65: 65: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 65: 65: chain #res #atoms 65: 65: 1 'P' 71 1527 65: 65: 2 'Q' 71 1527 65: 65: 3 'Q' 7 7 65: 65: 4 ' ' 10 10 (only water) 65: 65: 5 ' ' 16 16 (only water) 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'P' (1527 atoms, 71 residues) 65: 65: Identified residue G1 as a starting terminus. 65: 65: Identified residue U71 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 71 residues with 2297 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 2481, now 2481 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 6605 dihedrals, 183 impropers, 4434 angles 65: 5827 pairs, 2481 bonds and 0 virtual sites 65: 65: Total mass 22984.514 a.m.u. 65: 65: Total charge -71.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'Q' (1527 atoms, 71 residues) 65: 65: Identified residue G1 as a starting terminus. 65: 65: Identified residue U71 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 71 residues with 2297 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 2481, now 2481 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 6605 dihedrals, 183 impropers, 4434 angles 65: 5827 pairs, 2481 bonds and 0 virtual sites 65: 65: Total mass 22984.514 a.m.u. 65: 65: Total charge -71.000 e 65: 65: Writing topology 65: 65: Processing chain 3 'Q' (7 atoms, 7 residues) 65: 65: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 65: 65: Disabling further notes about ions. 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 7 residues with 7 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: No bonds 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 0 angles 65: 0 pairs, 0 bonds and 0 virtual sites 65: 65: Total mass 170.135 a.m.u. 65: 65: Total charge 14.000 e 65: 65: Writing topology 65: 65: Processing chain 4 (10 atoms, 10 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 10 residues with 30 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 30, now 30 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 30 angles 65: 0 pairs, 30 bonds and 0 virtual sites 65: 65: Total mass 180.154 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Processing chain 5 (16 atoms, 16 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain m9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: olecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 48 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 48, now 48 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 48 angles 65: 0 pairs, 48 bonds and 0 virtual sites 65: 65: Total mass 288.246 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Including chain 1 in system: 2297 atoms 71 residues 65: 65: Including chain 2 in system: 2297 atoms 71 residues 65: 65: Including chain 3 in system: 7 atoms 7 residues 65: 65: Including chain 4 in system: 30 atoms 10 residues 65: 65: Including chain 5 in system: 48 atoms 16 residues 65: 65: Now there are 4679 atoms and 175 residues 65: 65: Total mass in system 46607.562 a.m.u. 65: 65: Total charge in system -128.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (917 ms) 65: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 2325 pairs 65: Before cleaning: 2325 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 65: Read 'CARNOCYCLIN-A', 413 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 60 413 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (413 atoms, 60 residues) 65: 65: Identified residue LEU1 as a starting terminus. 65: 65: Identified residue LEU60 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 60 residues with 878 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 880, now 880 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 60 cmap torsion pairs 65: 65: There are 2325 dihedrals, 137 impropers, 1614 angles 65: 2319 pairs, 880 bonds and 0 virtual sites 65: 65: Total mass 5866.087 a.m.u. 65: 65: Total charge 4.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (203 ms) 65: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: WARNING: all CONECT records are ignored 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 12080 pairs 65: Before cleaning: 13210 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 65: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Moved all the water blocks to the end 65: 65: Merged chains into joint molecule definitions at 2 places. 65: 65: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 65: 65: chain #res #atoms 65: 65: 1 'P' 149 3061 65: 65: 2 ' ' 10 10 (only water) 65: 65: 3 ' ' 16 16 (only water) 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'P' (3061 atoms, 149 residues) 65: 65: Identified residue G1 as a starting terminus. 65: 65: Identified residue U71 as a ending terminus. 65: 65: Identified residue G1 as a starting terminus. 65: 65: Identified residue U71 as a ending terminus. 65: 65: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 65: 65: Disabling further notes about ions. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 149 residues with 4601 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 4962, now 4962 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 13210 dihedrals, 366 impropers, 8868 angles 65: 11654 pairs, 4962 bonds and 0 virtual sites 65: 65: Total mass 46139.162 a.m.u. 65: 65: Total charge -128.000 e 65: 65: Writing topology 65: 65: Processing chain 2 (10 atoms, 10 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 10 residues with 30 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 30, now 30 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 30 angles 65: 0 pairs, 30 bonds and 0 virtual sites 65: 65: Total mass 180.154 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Processing chain 3 (16 atoms, 16 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 48 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 48, now 48 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 48 angles 65: 0 pairs, 48 bonds and 0 virtual sites 65: 65: Total mass 288.246 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Including chain 1 in system: 4601 atoms 149 residues 65: 65: Including chain 2 in system: 30 atoms 10 residues 65: 65: Including chain 3 in system: 48 atoms 16 residues 65: 65: Now there are 4679 atoms and 175 residues 65: 65: Total mass in system 46607.562 a.m.u. 65: 65: Total charge in system -128.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (990 ms) 65: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 2325 pairs 65: Before cleaning: 2325 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 65: Read 'CARNOCYCLIN-A', 413 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 60 413 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (413 atoms, 60 residues) 65: 65: Identified residue LEU1 as a starting terminus. 65: 65: Identified residue LEU60 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 60 residues with 878 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 880, now 880 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 60 cmap torsion pairs 65: 65: There are 2325 dihedrals, 137 impropers, 1614 angles 65: 2319 pairs, 880 bonds and 0 virtual sites 65: 65: Total mass 5866.087 a.m.u. 65: 65: Total charge 4.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (205 ms) 65: [----------] 4 tests from Cyclic/Pdb2gmxTest (2317 ms total) 65: 65: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest 65: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 233 pairs 65: Before cleaning: 243 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 2325 pairs 65: Before cleaning: 2325 dihedrals 65: Using the Amber96 force field in directory amber96.ff 65: 65: going to rename amber96.ff/aminoacids.r2b 65: 65: going to rename amber96.ff/dna.r2b 65: 65: going to rename amber96.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 65: Read 'Two cyclic peptides, one small one big', 460 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 2 chains and 0 blocks of water and 65 residues with 460 atoms 65: 65: chain #res #atoms 65: 65: 1 'C' 5 47 65: 65: 2 'A' 60 413 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber96) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'C' (47 atoms, 5 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 86 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 89, now 89 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 243 dihedrals, 23 impropers, 159 angles 65: 230 pairs, 89 bonds and 0 virtual sites 65: 65: Total mass 653.702 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'A' (413 atoms, 60 residues) 65: 65: Identified residue LEU1 as a starting terminus. 65: 65: Identified residue LEU60 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 60 residues with 878 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 880, now 880 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2325 dihedrals, 141 impropers, 1614 angles 65: 2319 pairs, 880 bonds and 0 virtual sites 65: 65: Total mass 5866.100 a.m.u. 65: 65: Total charge 4.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 86 atoms 5 residues 65: 65: Including chain 2 in system: 878 atoms 60 residues 65: 65: Now there are 964 atoms and 65 residues 65: 65: Total mass in system 6519.802 a.m.u. 65: 65: Total charge in system 4.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 65: 65: The Amber96 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file (222 ms) 65: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 188 pairs 65: Before cleaning: 198 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 233 pairs 65: Before cleaning: 243 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 233 pairs 65: Before cleaning: 243 dihedrals 65: Using the Amber96 force field in directory amber96.ff 65: 65: going to rename amber96.ff/aminoacids.r2b 65: 65: going to rename amber96.ff/dna.r2b 65: 65: going to rename amber96.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 65: Read 'One linear then two cyclic peptides', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 3 chains and 0 blocks of water and 14 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 'C' 4 38 65: 65: 2 'E' 5 47 65: 65: 3 'F' 5 47 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber96) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'C' (38 atoms, 4 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue TRP4 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 4 residues with 72 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 75, now 74 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 198 dihedrals, 18 impropers, 132 angles 65: 185 pairs, 74 bonds and 0 virtual sites 65: 65: Total mass 543.584 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'E' (47 atoms, 5 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 86 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 89, now 89 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 243 dihedrals, 23 impropers, 159 angles 65: 230 pairs, 89 bonds and 0 virtual sites 65: 65: Total mass 653.702 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Processing chain 3 'F' (47 atoms, 5 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 86 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 89, now 89 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 243 dihedrals, 23 impropers, 159 angles 65: 230 pairs, 89 bonds and 0 virtual sites 65: 65: Total mass 653.702 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 72 atoms 4 residues 65: 65: Including chain 2 in system: 86 atoms 5 residues 65: 65: Including chain 3 in system: 86 atoms 5 residues 65: 65: Now there are 244 atoms and 14 residues 65: 65: Total mass in system 1850.988 a.m.u. 65: 65: Total charge in system 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 65: 65: The Amber96 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file (89 ms) 65: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 2558 pairs 65: Before cleaning: 2568 dihedrals 65: Using the Amber96 force field in directory amber96.ff 65: 65: going to rename amber96.ff/aminoacids.r2b 65: 65: going to rename amber96.ff/dna.r2b 65: 65: going to rename amber96.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 65: Read 'Two cyclic peptides, one small one big', 460 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Merged chains into joint molecule definitions at 1 places. 65: 65: There are 1 chains and 0 blocks of water and 65 residues with 460 atoms 65: 65: chain #res #atoms 65: 65: 1 'C' 65 460 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber96) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'C' (460 atoms, 65 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Identified residue LEU1 as a starting terminus. 65: 65: Identified residue LEU60 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 65 residues with 964 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 969, now 969 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2568 dihedrals, 164 impropers, 1773 angles 65: 2549 pairs, 969 bonds and 0 virtual sites 65: 65: Total mass 6519.802 a.m.u. 65: 65: Total charge 4.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 65: 65: The Amber96 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file (202 ms) 65: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 654 pairs 65: Before cleaning: 684 dihedrals 65: Using the Amber96 force field in directory amber96.ff 65: 65: going to rename amber96.ff/aminoacids.r2b 65: 65: going to rename amber96.ff/dna.r2b 65: 65: going to rename amber96.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 65: Read 'One linear then two cyclic peptides', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Merged chains into joint molecule definitions at 2 places. 65: 65: There are 1 chains and 0 blocks of water and 14 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 'C' 14 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber96) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'C' (132 atoms, 14 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue TRP4 as a ending terminus. 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 14 residues with 244 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 253, now 252 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 684 dihedrals, 64 impropers, 450 angles 65: 645 pairs, 252 bonds and 0 virtual sites 65: 65: Total mass 1850.988 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 65: 65: The Amber96 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file (80 ms) 65: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest (596 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 55 tests from 9 test suites ran. (6976 ms total) 65: [ PASSED ] 55 tests. 65/103 Test #65: Pdb2gmx3Test .............................. Passed 7.01 sec test 66 Start 66: CorrelationsTest 66: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/CorrelationsTest.xml" 66: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/correlationfunctions/tests 66: Test timeout computed to be: 30 66: [==========] Running 21 tests from 3 test suites. 66: [----------] Global test environment set-up. 66: [----------] 10 tests from AutocorrTest 66: [ RUN ] AutocorrTest.EacNormal 66: [ OK ] AutocorrTest.EacNormal (6 ms) 66: [ RUN ] AutocorrTest.EacNoNormalize 66: [ OK ] AutocorrTest.EacNoNormalize (3 ms) 66: [ RUN ] AutocorrTest.EacCos 66: [ OK ] AutocorrTest.EacCos (5 ms) 66: [ RUN ] AutocorrTest.EacVector 66: [ OK ] AutocorrTest.EacVector (5 ms) 66: [ RUN ] AutocorrTest.EacRcross 66: [ OK ] AutocorrTest.EacRcross (2 ms) 66: [ RUN ] AutocorrTest.EacP0 66: [ OK ] AutocorrTest.EacP0 (6 ms) 66: [ RUN ] AutocorrTest.EacP1 66: [ OK ] AutocorrTest.EacP1 (6 ms) 66: [ RUN ] AutocorrTest.EacP2 66: [ OK ] AutocorrTest.EacP2 (10 ms) 66: [ RUN ] AutocorrTest.EacP3 66: [ OK ] AutocorrTest.EacP3 (5 ms) 66: [ RUN ] AutocorrTest.EacP4 66: [ OK ] AutocorrTest.EacP4 (6 ms) 66: [----------] 10 tests from AutocorrTest (61 ms total) 66: 66: [----------] 10 tests from ExpfitTest 66: [ RUN ] ExpfitTest.EffnEXP1 66: [ OK ] ExpfitTest.EffnEXP1 (2 ms) 66: [ RUN ] ExpfitTest.EffnEXP2 66: [ OK ] ExpfitTest.EffnEXP2 (1 ms) 66: [ RUN ] ExpfitTest.EffnEXPEXP 66: [ OK ] ExpfitTest.EffnEXPEXP (4 ms) 66: [ RUN ] ExpfitTest.EffnEXP5 66: [ OK ] ExpfitTest.EffnEXP5 (8 ms) 66: [ RUN ] ExpfitTest.EffnEXP7 66: [ OK ] ExpfitTest.EffnEXP7 (7 ms) 66: [ RUN ] ExpfitTest.EffnEXP9 66: [ OK ] ExpfitTest.EffnEXP9 (32 ms) 66: [ RUN ] ExpfitTest.EffnERF 66: [ OK ] ExpfitTest.EffnERF (5 ms) 66: [ RUN ] ExpfitTest.EffnERREST 66: [ OK ] ExpfitTest.EffnERREST (7 ms) 66: [ RUN ] ExpfitTest.EffnVAC 66: [ OK ] ExpfitTest.EffnVAC (16 ms) 66: [ RUN ] ExpfitTest.EffnPRES 66: [ OK ] ExpfitTest.EffnPRES (19 ms) 66: [----------] 10 tests from ExpfitTest (105 ms total) 66: 66: [----------] 1 test from ManyAutocorrelationTest 66: [ RUN ] ManyAutocorrelationTest.Empty 66: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 66: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 21 tests from 3 test suites ran. (179 ms total) 66: [ PASSED ] 21 tests. 66/103 Test #66: CorrelationsTest .......................... Passed 0.21 sec test 67 Start 67: AnalysisDataUnitTests 67: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/analysisdata/tests 67: Test timeout computed to be: 30 67: [==========] Running 69 tests from 14 test suites. 67: [----------] Global test environment set-up. 67: [----------] 3 tests from AnalysisDataInitializationTest 67: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 67: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 67: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 67: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 67: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 67: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 67: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 67: 67: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 67: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 67: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 67: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 67: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 67: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 67: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 67: [----------] 8 tests from AnalysisDataCommonTest/0 (3 ms total) 67: 67: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 67: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 67: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 67: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 67: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 67: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 67: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 67: [----------] 8 tests from AnalysisDataCommonTest/1 (4 ms total) 67: 67: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 67: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 67: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 67: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 67: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 67: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 67: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 67: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 67: [----------] 8 tests from AnalysisDataCommonTest/2 (5 ms total) 67: 67: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 67: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 67: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 67: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 67: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 67: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 67: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 67: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 67: [----------] 8 tests from AnalysisDataCommonTest/3 (5 ms total) 67: 67: [----------] 4 tests from AnalysisArrayDataTest 67: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 67: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 67: [ RUN ] AnalysisArrayDataTest.StorageWorks 67: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 67: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 67: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 67: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 67: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 67: [----------] 4 tests from AnalysisArrayDataTest (1 ms total) 67: 67: [----------] 6 tests from AverageModuleTest 67: [ RUN ] AverageModuleTest.BasicTest 67: [ OK ] AverageModuleTest.BasicTest (1 ms) 67: [ RUN ] AverageModuleTest.HandlesMultipointData 67: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 67: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 67: [ OK ] AverageModuleTest.HandlesMultipleDataSets (2 ms) 67: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 67: [ OK ] AverageModuleTest.HandlesDataSetAveraging (2 ms) 67: [ RUN ] AverageModuleTest.CanCustomizeXAxis 67: [ OK ] AverageModuleTest.CanCustomizeXAxis (2 ms) 67: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 67: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (1 ms) 67: [----------] 6 tests from AverageModuleTest (11 ms total) 67: 67: [----------] 2 tests from FrameAverageModuleTest 67: [ RUN ] FrameAverageModuleTest.BasicTest 67: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 67: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 67: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 67: [----------] 2 tests from FrameAverageModuleTest (2 ms total) 67: 67: [----------] 7 tests from AnalysisHistogramSettingsTest 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 67: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 67: 67: [----------] 2 tests from SimpleHistogramModuleTest 67: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 67: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (1 ms) 67: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 67: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 67: [----------] 2 tests from SimpleHistogramModuleTest (3 ms total) 67: 67: [----------] 3 tests from WeightedHistogramModuleTest 67: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 67: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (1 ms) 67: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 67: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (2 ms) 67: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 67: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (3 ms) 67: [----------] 3 tests from WeightedHistogramModuleTest (7 ms total) 67: 67: [----------] 3 tests from BinAverageModuleTest 67: [ RUN ] BinAverageModuleTest.ComputesCorrectly 67: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 67: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 67: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (2 ms) 67: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 67: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (2 ms) 67: [----------] 3 tests from BinAverageModuleTest (6 ms total) 67: 67: [----------] 4 tests from AbstractAverageHistogramTest 67: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 67: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (1 ms) 67: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 67: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 67: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 67: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 67: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 67: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (2 ms) 67: [----------] 4 tests from AbstractAverageHistogramTest (8 ms total) 67: 67: [----------] 3 tests from LifetimeModuleTest 67: [ RUN ] LifetimeModuleTest.BasicTest 67: [ OK ] LifetimeModuleTest.BasicTest (1 ms) 67: [ RUN ] LifetimeModuleTest.CumulativeTest 67: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 67: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 67: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (1 ms) 67: [----------] 3 tests from LifetimeModuleTest (4 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 69 tests from 14 test suites ran. (64 ms total) 67: [ PASSED ] 69 tests. 67/103 Test #67: AnalysisDataUnitTests ..................... Passed 0.09 sec test 68 Start 68: CoordinateIOTests 68: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/CoordinateIOTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/coordinateio/tests 68: Test timeout computed to be: 30 68: [==========] Running 67 tests from 20 test suites. 68: [----------] Global test environment set-up. 68: [----------] 1 test from OutputSelectorDeathTest 68: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (6 ms) 68: [----------] 1 test from OutputSelectorDeathTest (6 ms total) 68: 68: [----------] 5 tests from TrajectoryFrameWriterTest 68: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (3 ms) 68: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (3 ms) 68: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (2 ms) 68: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (5 ms) 68: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 68: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 68: [----------] 5 tests from TrajectoryFrameWriterTest (14 ms total) 68: 68: [----------] 5 tests from OutputAdapterContainer 68: [ RUN ] OutputAdapterContainer.MakeEmpty 68: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 68: [ RUN ] OutputAdapterContainer.AddAdapter 68: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 68: [ RUN ] OutputAdapterContainer.RejectBadAdapter 68: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 68: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 68: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 68: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 68: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 68: [----------] 5 tests from OutputAdapterContainer (0 ms total) 68: 68: [----------] 3 tests from RegisterFrameConverterTest 68: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 68: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 68: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 68: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 68: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 68: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 68: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 68: 68: [----------] 5 tests from FlagTest 68: [ RUN ] FlagTest.CanSetSimpleFlag 68: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 68: [ RUN ] FlagTest.CanAddNewBox 68: [ OK ] FlagTest.CanAddNewBox (0 ms) 68: [ RUN ] FlagTest.SetsImplicitPrecisionChange 68: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 68: [ RUN ] FlagTest.SetsImplicitStartTimeChange 68: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 68: [ RUN ] FlagTest.SetsImplicitTimeStepChange 68: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 68: [----------] 5 tests from FlagTest (0 ms total) 68: 68: [----------] 5 tests from SetAtomsTest 68: [ RUN ] SetAtomsTest.RemovesExistingAtoms 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] SetAtomsTest.RemovesExistingAtoms (2 ms) 68: [ RUN ] SetAtomsTest.AddsNewAtoms 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] SetAtomsTest.AddsNewAtoms (2 ms) 68: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (2 ms) 68: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (2 ms) 68: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (2 ms) 68: [----------] 5 tests from SetAtomsTest (14 ms total) 68: 68: [----------] 2 tests from SetBothTimeTest 68: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 68: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 68: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 68: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 68: [----------] 2 tests from SetBothTimeTest (0 ms total) 68: 68: [----------] 2 tests from SetStartTimeTest 68: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 68: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 68: [ RUN ] SetStartTimeTest.WorksWithZeroStart 68: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 68: [----------] 2 tests from SetStartTimeTest (0 ms total) 68: 68: [----------] 1 test from SetTimeStepTest 68: [ RUN ] SetTimeStepTest.SetTimeStepWorks 68: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 68: [----------] 1 test from SetTimeStepTest (0 ms total) 68: 68: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (2 ms) 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (2 ms) 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (2 ms) 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (2 ms) 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (2 ms) 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (2 ms) 68: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (17 ms total) 68: 68: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 68: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (2 ms) 68: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (2 ms) 68: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (2 ms) 68: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (8 ms total) 68: 68: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 68: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 68: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 68: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 68: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 68: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 68: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 68: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 68: 68: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 68: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (6 ms) 68: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (6 ms) 68: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (6 ms) 68: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (6 ms) 68: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (25 ms total) 68: 68: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 68: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (2 ms) 68: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (2 ms) 68: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (2 ms) 68: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (8 ms total) 68: 68: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 68: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 68: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 68: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 68: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 68: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 68: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 68: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 68: 68: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 68: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (2 ms) 68: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (2 ms) 68: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (5 ms total) 68: 68: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 68: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 68: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 68: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 68: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 68: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 68: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 68: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 68: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 68: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 68: 68: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 68: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (2 ms) 68: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (2 ms) 68: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (5 ms total) 68: 68: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 68: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 68: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 68: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 68: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 68: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 68: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 68: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 68: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 68: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 68: 68: [----------] 4 tests from ModuleSupported/NoOptionalOutput 68: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (2 ms) 68: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (2 ms) 68: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (2 ms) 68: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (3 ms) 68: [----------] 4 tests from ModuleSupported/NoOptionalOutput (11 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 67 tests from 20 test suites ran. (120 ms total) 68: [ PASSED ] 67 tests. 68/103 Test #68: CoordinateIOTests ......................... Passed 0.15 sec test 69 Start 69: TrajectoryAnalysisUnitTests 69: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests 69: Test timeout computed to be: 1920 69: [==========] Running 394 tests from 21 test suites. 69: [----------] Global test environment set-up. 69: [----------] 11 tests from AngleModuleTest 69: [ RUN ] AngleModuleTest.ComputesSimpleAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesSimpleAngles (7 ms) 69: [ RUN ] AngleModuleTest.ComputesDihedrals 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesDihedrals (3 ms) 69: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesVectorPairAngles (3 ms) 69: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (4 ms) 69: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (4 ms) 69: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (4 ms) 69: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system for different angles', 33 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (3 ms) 69: [ RUN ] AngleModuleTest.ComputesMultipleAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesMultipleAngles (3 ms) 69: [ RUN ] AngleModuleTest.HandlesDynamicSelections 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.HandlesDynamicSelections (3 ms) 69: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (3 ms) 69: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (3 ms) 69: [----------] 11 tests from AngleModuleTest (47 ms total) 69: 69: [----------] 5 tests from ClustsizeTest 69: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 69: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 69: There is one group in the index 69: '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Total number of atoms in clusters = 24 69: cmid: 2, cmax: 4, max_size: 6 69: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 69: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (3 ms) 69: [ RUN ] ClustsizeTest.NoMolShortCutoff 69: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 69: There is one group in the index 69: '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Total number of atoms in clusters = 24 69: cmid: 1, cmax: 6, max_size: 6 69: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 69: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (3 ms) 69: [ RUN ] ClustsizeTest.MolDefaultCutoff 69: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Total number of atoms in clusters = 8 69: cmid: 2, cmax: 4, max_size: 2 69: 50%100%cmid: 2, cmax: 6, max_size: 2 69: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (4 ms) 69: [ RUN ] ClustsizeTest.MolShortCutoff 69: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Total number of atoms in clusters = 8 69: cmid: 1, cmax: 6, max_size: 2 69: 50%100%cmid: 2, cmax: 6, max_size: 2 69: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (4 ms) 69: [ RUN ] ClustsizeTest.MolCSize 69: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Total number of atoms in clusters = 8 69: cmid: 2, cmax: 4, max_size: 2 69: 50%100%cmid: 2, cmax: 6, max_size: 2 69: 50%100%[ OK ] ClustsizeTest.MolCSize (3 ms) 69: [----------] 5 tests from ClustsizeTest (19 ms total) 69: 69: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 69: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 69: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (1 ms) 69: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 8 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (3 ms) 69: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 8 atoms. 69: Reading frame 0 time 0.000 [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (3 ms) 69: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 69: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 69: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (9 ms total) 69: 69: [----------] 4 tests from ConvertTrjModuleTest 69: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (15 ms) 69: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (13 ms) 69: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (3 ms) 69: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (3 ms) 69: [----------] 4 tests from ConvertTrjModuleTest (35 ms total) 69: 69: [----------] 6 tests from DistanceModuleTest 69: [ RUN ] DistanceModuleTest.ComputesDistances 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: atomname S1 S2: 69: Number of samples: 5 69: Average distance: 1.43246 nm 69: Standard deviation: 0.96700 nm 69: [ OK ] DistanceModuleTest.ComputesDistances (4 ms) 69: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: atomname S1 S2: 69: Number of samples: 5 69: Average distance: 1.43246 nm 69: Standard deviation: 0.96700 nm 69: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 69: Number of samples: 4 69: Average distance: 1.81066 nm 69: Standard deviation: 0.79289 nm 69: [ OK ] DistanceModuleTest.ComputesMultipleDistances (4 ms) 69: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: atomname S1 S2 and res_cog x < 2.8: 69: Number of samples: 3 69: Average distance: 1.72076 nm 69: Standard deviation: 1.24839 nm 69: [ OK ] DistanceModuleTest.HandlesDynamicSelections (4 ms) 69: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: Contacts: 69: Number of samples: 2 69: Average distance: 1.00000 nm 69: Standard deviation: 0.00000 nm 69: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (13 ms) 69: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: SuccessiveContacts: 69: Number of samples: 2 69: Average distance: 1.00000 nm 69: Standard deviation: 0.00000 nm 69: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (14 ms) 69: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: ManyContacts: 69: Number of samples: 10 69: Average distance: 1.82913 nm 69: Standard deviation: 0.78478 nm 69: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (13 ms) 69: [----------] 6 tests from DistanceModuleTest (57 ms total) 69: 69: [----------] 2 tests from ExtractClusterModuleTest 69: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 69: trr version: GMX_trn_file (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 69: Analyzed 26 frames, last time 0.050 69: There are 8 clusters containing 26 structures, highest framenr is 25 69: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (8 ms) 69: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 69: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 69: Analyzed 26 frames, last time 0.050 69: There are 8 clusters containing 26 structures, highest framenr is 25 69: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (5 ms) 69: [----------] 2 tests from ExtractClusterModuleTest (13 ms total) 69: 69: [----------] 2 tests from FreeVolumeModuleTest 69: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for 40 particles. These were set to zero. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: cutoff = 0.18 nm 69: probe_radius = 0 nm 69: seed = 13 69: ninsert = 1000 probes per nm^3 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 69: Spoel, Luciano T. Costa 69: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 69: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 69: Environ. Sci. Technol. (2013) 69: https://doi.org/10.1021/es4020986 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Free volume 38.02 +/- 0.00 % 69: Total volume 68.92 +/- 0.00 nm^3 69: Number of molecules 340 total mass 63491.38 Dalton 69: Average molar mass: 186.74 Dalton 69: Density rho: 1529.71 +/- 0.00 nm^3 69: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 69: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 69: Fractional free volume 0.194 +/- 0.000 69: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (146 ms) 69: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: cutoff = 0.18 nm 69: probe_radius = 0 nm 69: seed = 17 69: ninsert = 1000 probes per nm^3 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 69: Spoel, Luciano T. Costa 69: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 69: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 69: Environ. Sci. Technol. (2013) 69: https://doi.org/10.1021/es4020986 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Free volume 38.48 +/- 0.00 % 69: Total volume 68.92 +/- 0.00 nm^3 69: Number of molecules 340 total mass 63491.38 Dalton 69: Average molar mass: 186.74 Dalton 69: Density rho: 1529.71 +/- 0.00 nm^3 69: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 69: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 69: Fractional free volume 0.200 +/- 0.000 69: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (194 ms) 69: [----------] 2 tests from FreeVolumeModuleTest (341 ms total) 69: 69: [----------] 13 tests from MsdModuleTest 69: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 69: Analyzed 10 frames, last time 9.000 69: [ OK ] MsdModuleTest.threeDimensionalDiffusion (48 ms) 69: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 69: Analyzed 10 frames, last time 9.000 69: [ OK ] MsdModuleTest.twoDimensionalDiffusion (3 ms) 69: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 69: Analyzed 10 frames, last time 9.000 69: [ OK ] MsdModuleTest.oneDimensionalDiffusion (3 ms) 69: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 69: Analyzed 10 frames, last time 9.000 69: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (4 ms) 69: [ RUN ] MsdModuleTest.multipleGroupsWork 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 69: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 69: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to -1376518513 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.multipleGroupsWork (45 ms) 69: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 0.100 69: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 69: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 69: Analyzed 21 frames, last time 2.000 69: Setting the LD random seed to 1062988735 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (43 ms) 69: [ RUN ] MsdModuleTest.trestartLessThanDt 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1612480561 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.trestartLessThanDt (35 ms) 69: [ RUN ] MsdModuleTest.trestartGreaterThanDt 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to -829542409 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.trestartGreaterThanDt (41 ms) 69: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -94404619 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (35 ms) 69: [ RUN ] MsdModuleTest.molTest 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to -390402297 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.molTest (41 ms) 69: [ RUN ] MsdModuleTest.beginFit 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 69: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 69: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to 1005583869 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.beginFit (40 ms) 69: [ RUN ] MsdModuleTest.endFit 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 69: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 69: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to 1757380091 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.endFit (40 ms) 69: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: NOTE: You provided an index file 69: /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 69: (with -n), but it was not used by any selection. 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 69: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 69: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to -288129025 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (45 ms) 69: [----------] 13 tests from MsdModuleTest (430 ms total) 69: 69: [----------] 9 tests from PairDistanceModuleTest 69: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesAllDistances (6 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (16 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (7 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (4 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (3 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (8 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (7 ms) 69: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (18 ms) 69: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (3 ms) 69: [----------] 9 tests from PairDistanceModuleTest (75 ms total) 69: 69: [----------] 5 tests from RdfModuleTest 69: [ RUN ] RdfModuleTest.BasicTest 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] RdfModuleTest.BasicTest (44 ms) 69: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 69: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (40 ms) 69: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (44 ms) 69: [ RUN ] RdfModuleTest.CalculatesSurf 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] RdfModuleTest.CalculatesSurf (16 ms) 69: [ RUN ] RdfModuleTest.CalculatesXY 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] RdfModuleTest.CalculatesXY (56 ms) 69: [----------] 5 tests from RdfModuleTest (203 ms total) 69: 69: [----------] 5 tests from SasaModuleTest 69: [ RUN ] SasaModuleTest.BasicTest 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 69: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 69: of Surface Area and Volume and to Dot Surface Contouring of Molecular 69: Assemblies 69: J. Comp. Chem. (1995) 69: https://doi.org/10.1002/jcc.540160303 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SasaModuleTest.BasicTest (20 ms) 69: [ RUN ] SasaModuleTest.HandlesSelectedResidues 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 69: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 69: of Surface Area and Volume and to Dot Surface Contouring of Molecular 69: Assemblies 69: J. Comp. Chem. (1995) 69: https://doi.org/10.1002/jcc.540160303 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SasaModuleTest.HandlesSelectedResidues (11 ms) 69: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 69: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 69: of Surface Area and Volume and to Dot Surface Contouring of Molecular 69: Assemblies 69: J. Comp. Chem. (1995) 69: https://doi.org/10.1002/jcc.540160303 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (7 ms) 69: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 69: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 69: of Surface Area and Volume and to Dot Surface Contouring of Molecular 69: Assemblies 69: J. Comp. Chem. (1995) 69: https://doi.org/10.1002/jcc.540160303 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (12 ms) 69: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 69: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 69: of Surface Area and Volume and to Dot Surface Contouring of Molecular 69: Assemblies 69: J. Comp. Chem. (1995) 69: https://doi.org/10.1002/jcc.540160303 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (12 ms) 69: [----------] 5 tests from SasaModuleTest (66 ms total) 69: 69: [----------] 9 tests from SelectModuleTest 69: [ RUN ] SelectModuleTest.BasicTest 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] SelectModuleTest.BasicTest (9 ms) 69: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (4 ms) 69: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (5 ms) 69: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (4 ms) 69: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (4 ms) 69: [ RUN ] SelectModuleTest.NormalizesSizes 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SelectModuleTest.NormalizesSizes (4 ms) 69: [ RUN ] SelectModuleTest.WritesResidueNumbers 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SelectModuleTest.WritesResidueNumbers (3 ms) 69: [ RUN ] SelectModuleTest.WritesResidueIndices 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SelectModuleTest.WritesResidueIndices (4 ms) 69: [ RUN ] SelectModuleTest.HandlesPrimeInAtomName 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SelectModuleTest.HandlesPrimeInAtomName (4 ms) 69: [----------] 9 tests from SelectModuleTest (47 ms total) 69: 69: [----------] 10 tests from SurfaceAreaTest 69: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 69: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 69: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 69: [ OK ] SurfaceAreaTest.ComputesTwoPoints (1 ms) 69: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 69: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (1 ms) 69: [ RUN ] SurfaceAreaTest.SurfacePoints12 69: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 69: [ RUN ] SurfaceAreaTest.SurfacePoints32 69: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 69: [ RUN ] SurfaceAreaTest.SurfacePoints42 69: [ OK ] SurfaceAreaTest.SurfacePoints42 (1 ms) 69: [ RUN ] SurfaceAreaTest.SurfacePoints122 69: [ OK ] SurfaceAreaTest.SurfacePoints122 (2 ms) 69: [ RUN ] SurfaceAreaTest.Computes100Points 69: [ OK ] SurfaceAreaTest.Computes100Points (2 ms) 69: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 69: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (5 ms) 69: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 69: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (5 ms) 69: [----------] 10 tests from SurfaceAreaTest (23 ms total) 69: 69: [----------] 4 tests from TopologyInformation 69: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 69: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 69: [ RUN ] TopologyInformation.WorksWithGroFile 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TopologyInformation.WorksWithGroFile (2 ms) 69: [ RUN ] TopologyInformation.WorksWithPdbFile 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TopologyInformation.WorksWithPdbFile (2 ms) 69: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file lysozyme.top, line 1465]: 69: System has non-zero total charge: 2.000000 69: Total charge should normally be an integer. See 69: https://manual.gromacs.org/current/user-guide/floating-point.html 69: for discussion on how close it should be to an integer. 69: 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 465.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 69: Setting the LD random seed to 2012142079 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 69: Analysing residue names: 69: There are: 10 Protein residues 69: Analysing Protein... 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (846 ms) 69: [----------] 4 tests from TopologyInformation (851 ms total) 69: 69: [----------] 4 tests from TrajectoryModuleTest 69: [ RUN ] TrajectoryModuleTest.BasicTest 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] TrajectoryModuleTest.BasicTest (40 ms) 69: [ RUN ] TrajectoryModuleTest.PlotsXOnly 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] TrajectoryModuleTest.PlotsXOnly (3 ms) 69: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (3 ms) 69: [ RUN ] TrajectoryModuleTest.HandlesNoForces 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] TrajectoryModuleTest.HandlesNoForces (3 ms) 69: [----------] 4 tests from TrajectoryModuleTest (51 ms total) 69: 69: [----------] 5 tests from UnionFinderTest 69: [ RUN ] UnionFinderTest.WorksEmpty 69: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 69: [ RUN ] UnionFinderTest.BasicMerges 69: [ OK ] UnionFinderTest.BasicMerges (0 ms) 69: [ RUN ] UnionFinderTest.LargerMerges 69: [ OK ] UnionFinderTest.LargerMerges (0 ms) 69: [ RUN ] UnionFinderTest.LongRightMerge 69: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 69: [ RUN ] UnionFinderTest.LongLeftMerge 69: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 69: [----------] 5 tests from UnionFinderTest (0 ms total) 69: 69: [----------] 1 test from MappedUnionFinderTest 69: [ RUN ] MappedUnionFinderTest.BasicMerges 69: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 69: [----------] 1 test from MappedUnionFinderTest (0 ms total) 69: 69: [----------] 192 tests from MoleculeTests/DsspModuleTest 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (40 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (37 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (53 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (37 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (40 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (32 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (31 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (31 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (31 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (31 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (46 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (31 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (30 ms) 69: [----------] 192 tests from MoleculeTests/DsspModuleTest (7168 ms total) 69: 69: [----------] 3 tests from GyrateTests/GyrateModuleTest 69: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (17 ms) 69: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (14 ms) 69: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (13 ms) 69: [----------] 3 tests from GyrateTests/GyrateModuleTest (46 ms total) 69: 69: [----------] 96 tests from HBondTests/HbondModuleTest 69: [ RUN ] HBondTests/HbondModuleTest.Works/0 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/0 (27 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/1 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/1 (27 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/2 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/2 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/3 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/3 (36 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/4 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/4 (26 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/5 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/5 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/6 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/6 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/7 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/7 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/8 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/8 (26 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/9 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/9 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/10 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/10 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/11 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/11 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/12 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/12 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/13 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/13 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/14 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/14 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/15 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/15 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/16 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/16 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/17 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/17 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/18 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/18 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/19 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/19 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/20 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/20 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/21 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/21 (26 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/22 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/22 (40 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/23 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/23 (28 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/24 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/24 (28 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/25 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/25 (26 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/26 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/26 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/27 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/27 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/28 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/28 (26 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/29 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/29 (27 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/30 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/30 (26 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/31 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/31 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/32 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/32 (176 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/33 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/33 (165 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/34 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/34 (195 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/35 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/35 (192 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/36 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/36 (198 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/37 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/37 (193 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/38 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/38 (194 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/39 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/39 (188 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/40 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/40 (199 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/41 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/41 (196 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/42 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/42 (194 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/43 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/43 (193 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/44 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/44 (199 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/45 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/45 (194 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/46 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/46 (193 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/47 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/47 (193 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/48 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/48 (195 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/49 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/49 (193 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/50 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/50 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/51 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/51 (192 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/52 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/52 (198 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/53 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/53 (193 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/54 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/54 (237 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/55 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/55 (157 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/56 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/56 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/57 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/57 (193 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/58 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/58 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/59 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/59 (204 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/60 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/60 (164 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/61 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/61 (191 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/62 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/62 (195 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/63 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/63 (192 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/64 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/64 (180 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/65 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/65 (179 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/66 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/66 (178 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/67 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/67 (179 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/68 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/68 (189 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/69 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/69 (187 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/70 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/70 (188 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/71 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/71 (188 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/72 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/72 (196 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/73 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/73 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/74 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/74 (199 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/75 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/75 (199 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/76 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/76 (200 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/77 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/77 (205 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/78 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/78 (171 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/79 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/79 (198 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/80 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/80 (178 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/81 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/81 (176 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/82 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/82 (163 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/83 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/83 (177 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/84 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/84 (185 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/85 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/85 (188 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/86 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/86 (186 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/87 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/87 (187 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/88 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/88 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/89 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/89 (164 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/90 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/90 (200 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/91 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/91 (199 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/92 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/92 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/93 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/93 (198 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/94 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/94 (198 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/95 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/95 (196 ms) 69: [----------] 96 tests from HBondTests/HbondModuleTest (14981 ms total) 69: 69: [----------] 4 tests from MoleculeTests/ScatteringModule 69: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 69: Method for calculating small-angle neutron scattering spectra using all-atom 69: molecular dynamics trajectories 69: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 69: https://doi.org/10.1134/S1027451013060372 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (59 ms) 69: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 69: Method for calculating small-angle neutron scattering spectra using all-atom 69: molecular dynamics trajectories 69: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 69: https://doi.org/10.1134/S1027451013060372 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: D. T. Cromer, J. B. Mann 69: X-ray scattering factors computed from numerical Hartree-Fock wave functions 69: Acta Cryst. A (1968) 69: https://doi.org/10.1107/S0567739468000550 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (662 ms) 69: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 69: Method for calculating small-angle neutron scattering spectra using all-atom 69: molecular dynamics trajectories 69: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 69: https://doi.org/10.1134/S1027451013060372 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (54 ms) 69: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 69: Method for calculating small-angle neutron scattering spectra using all-atom 69: molecular dynamics trajectories 69: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 69: https://doi.org/10.1134/S1027451013060372 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: D. T. Cromer, J. B. Mann 69: X-ray scattering factors computed from numerical Hartree-Fock wave functions 69: Acta Cryst. A (1968) 69: https://doi.org/10.1107/S0567739468000550 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (149 ms) 69: [----------] 4 tests from MoleculeTests/ScatteringModule (932 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 394 tests from 21 test suites ran. (25404 ms total) 69: [ PASSED ] 394 tests. 69/103 Test #69: TrajectoryAnalysisUnitTests ............... Passed 25.46 sec test 70 Start 70: EnergyAnalysisUnitTests 70: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests 70: Test timeout computed to be: 30 70: [==========] Running 12 tests from 5 test suites. 70: [----------] Global test environment set-up. 70: [----------] 2 tests from EnergyTermTest 70: [ RUN ] EnergyTermTest.ConstructWorks 70: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 70: [ RUN ] EnergyTermTest.AddFrameWorks 70: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 70: [----------] 2 tests from EnergyTermTest (0 ms total) 70: 70: [----------] 1 test from DhdlTest 70: [ RUN ] DhdlTest.ExtractDhdl 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 70: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 70: Note: file tpx version 110, software tpx version 138 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 70: 70: 70: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 70: [ OK ] DhdlTest.ExtractDhdl (52 ms) 70: [----------] 1 test from DhdlTest (53 ms total) 70: 70: [----------] 1 test from OriresTest 70: [ RUN ] OriresTest.ExtractOrires 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 70: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 70: Note: file tpx version 111, software tpx version 138 70: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 70: End your selection with 0 70: Selecting all 7 orientation restraints 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 70: [ OK ] OriresTest.ExtractOrires (23 ms) 70: [----------] 1 test from OriresTest (23 ms total) 70: 70: [----------] 5 tests from EnergyTest 70: [ RUN ] EnergyTest.ExtractEnergy 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: 70: Select the terms you want from the following list by 70: selecting either (part of) the name or the number or a combination. 70: End your selection with an empty line or a zero. 70: ------------------------------------------------------------------- 70: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 70: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 70: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 70: 13 Box-Z 14 Volume 15 Density 16 pV 70: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 70: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 70: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 70: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 70: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 70: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 70: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 70: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 70: [ OK ] EnergyTest.ExtractEnergy (5 ms) 70: [ RUN ] EnergyTest.ExtractEnergyByNumber 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: 70: Select the terms you want from the following list by 70: selecting either (part of) the name or the number or a combination. 70: End your selection with an empty line or a zero. 70: ------------------------------------------------------------------- 70: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 70: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 70: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 70: 13 Box-Z 14 Volume 15 Density 16 pV 70: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 70: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 70: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 70: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 70: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 70: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 70: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 70: Pres. DC -268.49 3 8.52175 13.2804 (bar) 70: [ OK ] EnergyTest.ExtractEnergyByNumber (4 ms) 70: [ RUN ] EnergyTest.ExtractEnergyMixed 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: 70: Select the terms you want from the following list by 70: selecting either (part of) the name or the number or a combination. 70: End your selection with an empty line or a zero. 70: ------------------------------------------------------------------- 70: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 70: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 70: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 70: 13 Box-Z 14 Volume 15 Density 16 pV 70: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 70: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 70: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 70: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 70: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 70: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 70: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 70: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 70: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 70: [ OK ] EnergyTest.ExtractEnergyMixed (5 ms) 70: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 70: 70: Select the terms you want from the following list by 70: selecting either (part of) the name or the number or a combination. 70: End your selection with an empty line or a zero. 70: ------------------------------------------------------------------- 70: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 70: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 70: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 70: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 70: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 70: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 70: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 70: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 70: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 70: 37 1/Viscosity 38 T-System 39 Lamb-System 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 70: 70: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 70: All statistics are over 3 points (frames) 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 70: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (1 ms) 70: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 70: 70: Select the terms you want from the following list by 70: selecting either (part of) the name or the number or a combination. 70: End your selection with an empty line or a zero. 70: ------------------------------------------------------------------- 70: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 70: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 70: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 70: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 70: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 70: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 70: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 70: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 70: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 70: 37 1/Viscosity 38 T-System 39 Lamb-System 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 70: 70: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 70: All statistics are over 3 points (frames) 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 70: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 70: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (1 ms) 70: [----------] 5 tests from EnergyTest (19 ms total) 70: 70: [----------] 3 tests from ViscosityTest 70: [ RUN ] ViscosityTest.EinsteinViscosity 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Pres-XX 20.2092 65 717.193 185.978 (bar) 70: Pres-XY -47.7351 39 372.522 207.456 (bar) 70: Pres-XZ 11.477 31 379.79 6.80818 (bar) 70: Pres-YX -47.7106 39 372.525 207.5 (bar) 70: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 70: Pres-YZ -41.3534 45 401.216 114.663 (bar) 70: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 70: Pres-ZY -41.3119 45 401.196 114.743 (bar) 70: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 70: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 70: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 70: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 70: 70: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 70: [ OK ] ViscosityTest.EinsteinViscosity (11 ms) 70: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Pres-XX 20.2092 65 717.193 185.978 (bar) 70: Pres-XY -47.7351 39 372.522 207.456 (bar) 70: Pres-XZ 11.477 31 379.79 6.80818 (bar) 70: Pres-YX -47.7106 39 372.525 207.5 (bar) 70: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 70: Pres-YZ -41.3534 45 401.216 114.663 (bar) 70: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 70: Pres-ZY -41.3119 45 401.196 114.743 (bar) 70: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 70: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 70: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 70: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 70: 70: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 70: [ OK ] ViscosityTest.EinsteinViscosityIntegral (9 ms) 70: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Pres-XX 20.2092 65 717.193 185.978 (bar) 70: Pres-XY -47.7351 39 372.522 207.456 (bar) 70: Pres-XZ 11.477 31 379.79 6.80818 (bar) 70: Pres-YX -47.7106 39 372.525 207.5 (bar) 70: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 70: Pres-YZ -41.3534 45 401.216 114.663 (bar) 70: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 70: Pres-ZY -41.3119 45 401.196 114.743 (bar) 70: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 70: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 70: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 70: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 70: 70: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 70: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (10 ms) 70: [----------] 3 tests from ViscosityTest (32 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 12 tests from 5 test suites ran. (128 ms total) 70: [ PASSED ] 12 tests. 70/103 Test #70: EnergyAnalysisUnitTests ................... Passed 0.15 sec test 71 Start 71: ToolUnitTests 71: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/ToolUnitTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests 71: Test timeout computed to be: 1920 71: [==========] Running 70 tests from 8 test suites. 71: [----------] Global test environment set-up. 71: [----------] 2 tests from DumpTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Setting the LD random seed to -1057521669 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: [ RUN ] DumpTest.WorksWithTpr 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 71: inputrec: 71: integrator = md 71: tinit = 0 71: dt = 0.001 71: nsteps = 0 71: init-step = 0 71: simulation-part = 1 71: mts = false 71: mass-repartition-factor = 1 71: comm-mode = Linear 71: nstcomm = 100 71: bd-fric = 0 71: ld-seed = -1057521669 71: emtol = 10 71: emstep = 0.01 71: niter = 20 71: fcstep = 0 71: nstcgsteep = 1000 71: nbfgscorr = 10 71: rtpi = 0.05 71: nstxout = 0 71: nstvout = 0 71: nstfout = 0 71: nstlog = 1000 71: nstcalcenergy = 100 71: nstenergy = 1000 71: nstxout-compressed = 0 71: compressed-x-precision = 1000 71: cutoff-scheme = Verlet 71: nstlist = 10 71: pbc = xyz 71: periodic-molecules = false 71: verlet-buffer-tolerance = -1 71: verlet-buffer-pressure-tolerance = 0.5 71: rlist = 1.1 71: coulombtype = Cut-off 71: coulomb-modifier = Potential-shift 71: rcoulomb-switch = 0 71: rcoulomb = 1 71: epsilon-r = 1 71: epsilon-rf = inf 71: vdw-type = Cut-off 71: vdw-modifier = Potential-shift 71: rvdw-switch = 0 71: rvdw = 1 71: DispCorr = No 71: table-extension = 1 71: fourierspacing = 0.12 71: fourier-nx = 0 71: fourier-ny = 0 71: fourier-nz = 0 71: pme-order = 4 71: ewald-rtol = 1e-05 71: ewald-rtol-lj = 0.001 71: lj-pme-comb-rule = Geometric 71: ewald-geometry = 3d 71: epsilon-surface = 0 71: ensemble-temperature-setting = not available 71: tcoupl = No 71: nsttcouple = -1 71: nh-chain-length = 0 71: print-nose-hoover-chain-variables = false 71: pcoupl = No 71: refcoord-scaling = No 71: posres-com: not available 71: posres-comB: not available 71: QMMM = false 71: qm-opts: 71: ngQM = 0 71: constraint-algorithm = Lincs 71: continuation = false 71: Shake-SOR = false 71: shake-tol = 0.0001 71: lincs-order = 4 71: lincs-iter = 1 71: lincs-warnangle = 30 71: nwall = 0 71: wall-type = 9-3 71: wall-r-linpot = -1 71: wall-atomtype[0] = -1 71: wall-atomtype[1] = -1 71: wall-density[0] = 0 71: wall-density[1] = 0 71: wall-ewald-zfac = 3 71: pull = false 71: awh = false 71: rotation = false 71: interactiveMD = false 71: disre = No 71: disre-weighting = Conservative 71: disre-mixed = false 71: dr-fc = 1000 71: dr-tau = 0 71: nstdisreout = 100 71: orire-fc = 0 71: orire-tau = 0 71: nstorireout = 100 71: free-energy = no 71: cos-acceleration = 0 71: deform (3x3): 71: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: simulated-tempering = false 71: swapcoords = no 71: userint1 = 0 71: userint2 = 0 71: userint3 = 0 71: userint4 = 0 71: userreal1 = 0 71: userreal2 = 0 71: userreal3 = 0 71: userreal4 = 0 71: applied-forces: 71: electric-field: 71: x: 71: E0 = 0 71: omega = 0 71: t0 = 0 71: sigma = 0 71: y: 71: E0 = 0 71: omega = 0 71: t0 = 0 71: sigma = 0 71: z: 71: E0 = 0 71: omega = 0 71: t0 = 0 71: sigma = 0 71: density-guided-simulation: 71: active = false 71: group = protein 71: similarity-measure = inner-product 71: atom-spreading-weight = unity 71: force-constant = 1e+09 71: gaussian-transform-spreading-width = 0.2 71: gaussian-transform-spreading-range-in-multiples-of-width = 4 71: reference-density-filename = reference.mrc 71: nst = 1 71: normalize-densities = true 71: adaptive-force-scaling = false 71: adaptive-force-scaling-time-constant = 4 71: shift-vector = 71: transformation-matrix = 71: qmmm-cp2k: 71: active = false 71: qmgroup = System 71: qmmethod = PBE 71: qmfilenames = 71: qmcharge = 0 71: qmmultiplicity = 1 71: colvars: 71: active = false 71: configfile = 71: seed = -1 71: nnpot: 71: active = false 71: modelfile = model.pt 71: input-group = System 71: link-type = H 71: link-distance = 0.1 71: pair-cutoff = 0 71: embedding = mechanical 71: nnp-charge = 0 71: model-input1 = 71: model-input2 = 71: model-input3 = 71: model-input4 = 71: model-input5 = 71: model-input6 = 71: model-input7 = 71: model-input8 = 71: model-input9 = 71: fast-multipole-method: 71: fmm: 71: backend = inactive 71: exafmm-order = 6 71: exafmm-direct-range = 2 71: exafmm-direct-provider = GROMACS 71: exafmm-tree-type = uniform 71: exafmm-tree-depth = 0 71: exafmm-max-particles-per-cell = 0 71: fmsolvr-order = 8 71: fmsolvr-direct-range = 1 71: fmsolvr-direct-provider = FMM 71: fmsolvr-dipole-compensation = true 71: fmsolvr-tree-depth = 3 71: fmsolvr-sparse = false 71: grpopts: 71: nrdf: 465 71: ref-t: 0 71: tau-t: 0 71: annealing: No 71: annealing-npoints: 0 71: acc: 0 0 0 71: nfreeze: N N N 71: energygrp-flags[ 0]: 0 71: header: 71: bIr = present 71: bBox = present 71: bTop = present 71: bX = present 71: bV = present 71: bF = not present 71: natoms = 156 71: lambda = 0.000000e+00 71: buffer size = 47154 71: topology: 71: name="First 10 residues from 1AKI" 71: #atoms = 156 71: #molblock = 1 71: molblock (0): 71: moltype = 0 "Protein_chain_B" 71: #molecules = 1 71: #posres_xA = 0 71: #posres_xB = 0 71: bIntermolecularInteractions = false 71: ffparams: 71: atnr=10 71: ntypes=212 71: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 71: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 71: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 71: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 71: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 71: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 71: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 71: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 71: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 71: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 71: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 71: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 71: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 71: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 71: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 71: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 71: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 71: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 71: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 71: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 71: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 71: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 71: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 71: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 71: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 71: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 71: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 71: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 71: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 71: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 71: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 71: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 71: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 71: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 71: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 71: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 71: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 71: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 71: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 71: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 71: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 71: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 71: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 71: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 71: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 71: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 71: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 71: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 71: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 71: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 71: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 71: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 71: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 71: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 71: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 71: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 71: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 71: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 71: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 71: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 71: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 71: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 71: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 71: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 71: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 71: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 71: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 71: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 71: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 71: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 71: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 71: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 71: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 71: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 71: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 71: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 71: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 71: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 71: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 71: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 71: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 71: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 71: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 71: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 71: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 71: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 71: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 71: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 71: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 71: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 71: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 71: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 71: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 71: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 71: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 71: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 71: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 71: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 71: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 71: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 71: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 71: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 71: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 71: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 71: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 71: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 71: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 71: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 71: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 71: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 71: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 71: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 71: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 71: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 71: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 71: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 71: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 71: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 71: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 71: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 71: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 71: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 71: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 71: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 71: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 71: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 71: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 71: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 71: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 71: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 71: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 71: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 71: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 71: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 71: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 71: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 71: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 71: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 71: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 71: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 71: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 71: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 71: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 71: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 71: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 71: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 71: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 71: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 71: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 71: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 71: reppow = 12 71: fudgeQQ = 0.5 71: cmap 71: moltype (0): 71: name="Protein_chain_B" 71: atoms: 71: atom (156): 71: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 71: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 71: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 71: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 71: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 71: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 71: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 71: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 71: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 71: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 71: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 71: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 71: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 71: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 71: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 71: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 71: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 71: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 71: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 71: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 71: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 71: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 71: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 71: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 71: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 71: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 71: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 71: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 71: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 71: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 71: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 71: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 71: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 71: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 71: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 71: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 71: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 71: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 71: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 71: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 71: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 71: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 71: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 71: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 71: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 71: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 71: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 71: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 71: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 71: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 71: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 71: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 71: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 71: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 71: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 71: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 71: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 71: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 71: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 71: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 71: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 71: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 71: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 71: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 71: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 71: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 71: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 71: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 71: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 71: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 71: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 71: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 71: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 71: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 71: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 71: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 71: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 71: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 71: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 71: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 71: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 71: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 71: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 71: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 71: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 71: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 71: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 71: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 71: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 71: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 71: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 71: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 71: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 71: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 71: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 71: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 71: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 71: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 71: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 71: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 71: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 71: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 71: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 71: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 71: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 71: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 71: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 71: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 71: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 71: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 71: atom (156): 71: atom[0]={name="N"} 71: atom[1]={name="H1"} 71: atom[2]={name="H2"} 71: atom[3]={name="H3"} 71: atom[4]={name="CA"} 71: atom[5]={name="HA"} 71: atom[6]={name="CB"} 71: atom[7]={name="HB1"} 71: atom[8]={name="HB2"} 71: atom[9]={name="CG"} 71: atom[10]={name="HG1"} 71: atom[11]={name="HG2"} 71: atom[12]={name="CD"} 71: atom[13]={name="HD1"} 71: atom[14]={name="HD2"} 71: atom[15]={name="CE"} 71: atom[16]={name="HE1"} 71: atom[17]={name="HE2"} 71: atom[18]={name="NZ"} 71: atom[19]={name="HZ1"} 71: atom[20]={name="HZ2"} 71: atom[21]={name="HZ3"} 71: atom[22]={name="C"} 71: atom[23]={name="O"} 71: atom[24]={name="N"} 71: atom[25]={name="H"} 71: atom[26]={name="CA"} 71: atom[27]={name="HA"} 71: atom[28]={name="CB"} 71: atom[29]={name="HB"} 71: atom[30]={name="CG1"} 71: atom[31]={name="HG11"} 71: atom[32]={name="HG12"} 71: atom[33]={name="HG13"} 71: atom[34]={name="CG2"} 71: atom[35]={name="HG21"} 71: atom[36]={name="HG22"} 71: atom[37]={name="HG23"} 71: atom[38]={name="C"} 71: atom[39]={name="O"} 71: atom[40]={name="N"} 71: atom[41]={name="H"} 71: atom[42]={name="CA"} 71: atom[43]={name="HA"} 71: atom[44]={name="CB"} 71: atom[45]={name="HB1"} 71: atom[46]={name="HB2"} 71: atom[47]={name="CG"} 71: atom[48]={name="CD1"} 71: atom[49]={name="HD1"} 71: atom[50]={name="CD2"} 71: atom[51]={name="HD2"} 71: atom[52]={name="CE1"} 71: atom[53]={name="HE1"} 71: atom[54]={name="CE2"} 71: atom[55]={name="HE2"} 71: atom[56]={name="CZ"} 71: atom[57]={name="HZ"} 71: atom[58]={name="C"} 71: atom[59]={name="O"} 71: atom[60]={name="N"} 71: atom[61]={name="H"} 71: atom[62]={name="CA"} 71: atom[63]={name="HA1"} 71: atom[64]={name="HA2"} 71: atom[65]={name="C"} 71: atom[66]={name="O"} 71: atom[67]={name="N"} 71: atom[68]={name="H"} 71: atom[69]={name="CA"} 71: atom[70]={name="HA"} 71: atom[71]={name="CB"} 71: atom[72]={name="HB1"} 71: atom[73]={name="HB2"} 71: atom[74]={name="CG"} 71: atom[75]={name="HG1"} 71: atom[76]={name="HG2"} 71: atom[77]={name="CD"} 71: atom[78]={name="HD1"} 71: atom[79]={name="HD2"} 71: atom[80]={name="NE"} 71: atom[81]={name="HE"} 71: atom[82]={name="CZ"} 71: atom[83]={name="NH1"} 71: atom[84]={name="HH11"} 71: atom[85]={name="HH12"} 71: atom[86]={name="NH2"} 71: atom[87]={name="HH21"} 71: atom[88]={name="HH22"} 71: atom[89]={name="C"} 71: atom[90]={name="O"} 71: atom[91]={name="N"} 71: atom[92]={name="H"} 71: atom[93]={name="CA"} 71: atom[94]={name="HA"} 71: atom[95]={name="CB"} 71: atom[96]={name="HB1"} 71: atom[97]={name="HB2"} 71: atom[98]={name="SG"} 71: atom[99]={name="HG"} 71: atom[100]={name="C"} 71: atom[101]={name="O"} 71: atom[102]={name="N"} 71: atom[103]={name="H"} 71: atom[104]={name="CA"} 71: atom[105]={name="HA"} 71: atom[106]={name="CB"} 71: atom[107]={name="HB1"} 71: atom[108]={name="HB2"} 71: atom[109]={name="CG"} 71: atom[110]={name="HG1"} 71: atom[111]={name="HG2"} 71: atom[112]={name="CD"} 71: atom[113]={name="OE1"} 71: atom[114]={name="OE2"} 71: atom[115]={name="C"} 71: atom[116]={name="O"} 71: atom[117]={name="N"} 71: atom[118]={name="H"} 71: atom[119]={name="CA"} 71: atom[120]={name="HA"} 71: atom[121]={name="CB"} 71: atom[122]={name="HB1"} 71: atom[123]={name="HB2"} 71: atom[124]={name="CG"} 71: atom[125]={name="HG"} 71: atom[126]={name="CD1"} 71: atom[127]={name="HD11"} 71: atom[128]={name="HD12"} 71: atom[129]={name="HD13"} 71: atom[130]={name="CD2"} 71: atom[131]={name="HD21"} 71: atom[132]={name="HD22"} 71: atom[133]={name="HD23"} 71: atom[134]={name="C"} 71: atom[135]={name="O"} 71: atom[136]={name="N"} 71: atom[137]={name="H"} 71: atom[138]={name="CA"} 71: atom[139]={name="HA"} 71: atom[140]={name="CB"} 71: atom[141]={name="HB1"} 71: atom[142]={name="HB2"} 71: atom[143]={name="HB3"} 71: atom[144]={name="C"} 71: atom[145]={name="O"} 71: atom[146]={name="N"} 71: atom[147]={name="H"} 71: atom[148]={name="CA"} 71: atom[149]={name="HA"} 71: atom[150]={name="CB"} 71: atom[151]={name="HB1"} 71: atom[152]={name="HB2"} 71: atom[153]={name="HB3"} 71: atom[154]={name="C"} 71: atom[155]={name="O"} 71: type (156): 71: type[0]={name="opls_287",nameB="opls_287"} 71: type[1]={name="opls_290",nameB="opls_290"} 71: type[2]={name="opls_290",nameB="opls_290"} 71: type[3]={name="opls_290",nameB="opls_290"} 71: type[4]={name="opls_293B",nameB="opls_293B"} 71: type[5]={name="opls_140",nameB="opls_140"} 71: type[6]={name="opls_136",nameB="opls_136"} 71: type[7]={name="opls_140",nameB="opls_140"} 71: type[8]={name="opls_140",nameB="opls_140"} 71: type[9]={name="opls_136",nameB="opls_136"} 71: type[10]={name="opls_140",nameB="opls_140"} 71: type[11]={name="opls_140",nameB="opls_140"} 71: type[12]={name="opls_136",nameB="opls_136"} 71: type[13]={name="opls_140",nameB="opls_140"} 71: type[14]={name="opls_140",nameB="opls_140"} 71: type[15]={name="opls_292",nameB="opls_292"} 71: type[16]={name="opls_140",nameB="opls_140"} 71: type[17]={name="opls_140",nameB="opls_140"} 71: type[18]={name="opls_287",nameB="opls_287"} 71: type[19]={name="opls_290",nameB="opls_290"} 71: type[20]={name="opls_290",nameB="opls_290"} 71: type[21]={name="opls_290",nameB="opls_290"} 71: type[22]={name="opls_235",nameB="opls_235"} 71: type[23]={name="opls_236",nameB="opls_236"} 71: type[24]={name="opls_238",nameB="opls_238"} 71: type[25]={name="opls_241",nameB="opls_241"} 71: type[26]={name="opls_224B",nameB="opls_224B"} 71: type[27]={name="opls_140",nameB="opls_140"} 71: type[28]={name="opls_137",nameB="opls_137"} 71: type[29]={name="opls_140",nameB="opls_140"} 71: type[30]={name="opls_135",nameB="opls_135"} 71: type[31]={name="opls_140",nameB="opls_140"} 71: type[32]={name="opls_140",nameB="opls_140"} 71: type[33]={name="opls_140",nameB="opls_140"} 71: type[34]={name="opls_135",nameB="opls_135"} 71: type[35]={name="opls_140",nameB="opls_140"} 71: type[36]={name="opls_140",nameB="opls_140"} 71: type[37]={name="opls_140",nameB="opls_140"} 71: type[38]={name="opls_235",nameB="opls_235"} 71: type[39]={name="opls_236",nameB="opls_236"} 71: type[40]={name="opls_238",nameB="opls_238"} 71: type[41]={name="opls_241",nameB="opls_241"} 71: type[42]={name="opls_224B",nameB="opls_224B"} 71: type[43]={name="opls_140",nameB="opls_140"} 71: type[44]={name="opls_149",nameB="opls_149"} 71: type[45]={name="opls_140",nameB="opls_140"} 71: type[46]={name="opls_140",nameB="opls_140"} 71: type[47]={name="opls_145",nameB="opls_145"} 71: type[48]={name="opls_145",nameB="opls_145"} 71: type[49]={name="opls_146",nameB="opls_146"} 71: type[50]={name="opls_145",nameB="opls_145"} 71: type[51]={name="opls_146",nameB="opls_146"} 71: type[52]={name="opls_145",nameB="opls_145"} 71: type[53]={name="opls_146",nameB="opls_146"} 71: type[54]={name="opls_145",nameB="opls_145"} 71: type[55]={name="opls_146",nameB="opls_146"} 71: type[56]={name="opls_145",nameB="opls_145"} 71: type[57]={name="opls_146",nameB="opls_146"} 71: type[58]={name="opls_235",nameB="opls_235"} 71: type[59]={name="opls_236",nameB="opls_236"} 71: type[60]={name="opls_238",nameB="opls_238"} 71: type[61]={name="opls_241",nameB="opls_241"} 71: type[62]={name="opls_223B",nameB="opls_223B"} 71: type[63]={name="opls_140",nameB="opls_140"} 71: type[64]={name="opls_140",nameB="opls_140"} 71: type[65]={name="opls_235",nameB="opls_235"} 71: type[66]={name="opls_236",nameB="opls_236"} 71: type[67]={name="opls_238",nameB="opls_238"} 71: type[68]={name="opls_241",nameB="opls_241"} 71: type[69]={name="opls_224B",nameB="opls_224B"} 71: type[70]={name="opls_140",nameB="opls_140"} 71: type[71]={name="opls_136",nameB="opls_136"} 71: type[72]={name="opls_140",nameB="opls_140"} 71: type[73]={name="opls_140",nameB="opls_140"} 71: type[74]={name="opls_308",nameB="opls_308"} 71: type[75]={name="opls_140",nameB="opls_140"} 71: type[76]={name="opls_140",nameB="opls_140"} 71: type[77]={name="opls_307",nameB="opls_307"} 71: type[78]={name="opls_140",nameB="opls_140"} 71: type[79]={name="opls_140",nameB="opls_140"} 71: type[80]={name="opls_303",nameB="opls_303"} 71: type[81]={name="opls_304",nameB="opls_304"} 71: type[82]={name="opls_302",nameB="opls_302"} 71: type[83]={name="opls_300",nameB="opls_300"} 71: type[84]={name="opls_301",nameB="opls_301"} 71: type[85]={name="opls_301",nameB="opls_301"} 71: type[86]={name="opls_300",nameB="opls_300"} 71: type[87]={name="opls_301",nameB="opls_301"} 71: type[88]={name="opls_301",nameB="opls_301"} 71: type[89]={name="opls_235",nameB="opls_235"} 71: type[90]={name="opls_236",nameB="opls_236"} 71: type[91]={name="opls_238",nameB="opls_238"} 71: type[92]={name="opls_241",nameB="opls_241"} 71: type[93]={name="opls_224B",nameB="opls_224B"} 71: type[94]={name="opls_140",nameB="opls_140"} 71: type[95]={name="opls_206",nameB="opls_206"} 71: type[96]={name="opls_140",nameB="opls_140"} 71: type[97]={name="opls_140",nameB="opls_140"} 71: type[98]={name="opls_200",nameB="opls_200"} 71: type[99]={name="opls_204",nameB="opls_204"} 71: type[100]={name="opls_235",nameB="opls_235"} 71: type[101]={name="opls_236",nameB="opls_236"} 71: type[102]={name="opls_238",nameB="opls_238"} 71: type[103]={name="opls_241",nameB="opls_241"} 71: type[104]={name="opls_224B",nameB="opls_224B"} 71: type[105]={name="opls_140",nameB="opls_140"} 71: type[106]={name="opls_136",nameB="opls_136"} 71: type[107]={name="opls_140",nameB="opls_140"} 71: type[108]={name="opls_140",nameB="opls_140"} 71: type[109]={name="opls_274",nameB="opls_274"} 71: type[110]={name="opls_140",nameB="opls_140"} 71: type[111]={name="opls_140",nameB="opls_140"} 71: type[112]={name="opls_271",nameB="opls_271"} 71: type[113]={name="opls_272",nameB="opls_272"} 71: type[114]={name="opls_272",nameB="opls_272"} 71: type[115]={name="opls_235",nameB="opls_235"} 71: type[116]={name="opls_236",nameB="opls_236"} 71: type[117]={name="opls_238",nameB="opls_238"} 71: type[118]={name="opls_241",nameB="opls_241"} 71: type[119]={name="opls_224B",nameB="opls_224B"} 71: type[120]={name="opls_140",nameB="opls_140"} 71: type[121]={name="opls_136",nameB="opls_136"} 71: type[122]={name="opls_140",nameB="opls_140"} 71: type[123]={name="opls_140",nameB="opls_140"} 71: type[124]={name="opls_137",nameB="opls_137"} 71: type[125]={name="opls_140",nameB="opls_140"} 71: type[126]={name="opls_135",nameB="opls_135"} 71: type[127]={name="opls_140",nameB="opls_140"} 71: type[128]={name="opls_140",nameB="opls_140"} 71: type[129]={name="opls_140",nameB="opls_140"} 71: type[130]={name="opls_135",nameB="opls_135"} 71: type[131]={name="opls_140",nameB="opls_140"} 71: type[132]={name="opls_140",nameB="opls_140"} 71: type[133]={name="opls_140",nameB="opls_140"} 71: type[134]={name="opls_235",nameB="opls_235"} 71: type[135]={name="opls_236",nameB="opls_236"} 71: type[136]={name="opls_238",nameB="opls_238"} 71: type[137]={name="opls_241",nameB="opls_241"} 71: type[138]={name="opls_224B",nameB="opls_224B"} 71: type[139]={name="opls_140",nameB="opls_140"} 71: type[140]={name="opls_135",nameB="opls_135"} 71: type[141]={name="opls_140",nameB="opls_140"} 71: type[142]={name="opls_140",nameB="opls_140"} 71: type[143]={name="opls_140",nameB="opls_140"} 71: type[144]={name="opls_235",nameB="opls_235"} 71: type[145]={name="opls_236",nameB="opls_236"} 71: type[146]={name="opls_238",nameB="opls_238"} 71: type[147]={name="opls_241",nameB="opls_241"} 71: type[148]={name="opls_224B",nameB="opls_224B"} 71: type[149]={name="opls_140",nameB="opls_140"} 71: type[150]={name="opls_135",nameB="opls_135"} 71: type[151]={name="opls_140",nameB="opls_140"} 71: type[152]={name="opls_140",nameB="opls_140"} 71: type[153]={name="opls_140",nameB="opls_140"} 71: type[154]={name="opls_235",nameB="opls_235"} 71: type[155]={name="opls_236",nameB="opls_236"} 71: residue (10): 71: residue[0]={name="LYS", nr=1, ic=' '} 71: residue[1]={name="VAL", nr=2, ic=' '} 71: residue[2]={name="PHE", nr=3, ic=' '} 71: residue[3]={name="GLY", nr=4, ic=' '} 71: residue[4]={name="ARG", nr=5, ic=' '} 71: residue[5]={name="CYS", nr=6, ic=' '} 71: residue[6]={name="GLU", nr=7, ic=' '} 71: residue[7]={name="LEU", nr=8, ic=' '} 71: residue[8]={name="ALA", nr=9, ic=' '} 71: residue[9]={name="ALA", nr=10, ic=' '} 71: excls: 71: numLists=156 71: numElements=1828 71: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 71: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 71: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 71: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 71: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 71: 23, 24, 25, 26} 71: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 71: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 71: 14, 15, 22, 23, 24} 71: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 71: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 71: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 71: 16, 17, 18, 22} 71: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 71: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 71: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 71: 17, 18, 19, 20, 21} 71: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 71: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 71: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 71: 20, 21} 71: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 71: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 71: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 71: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 71: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 71: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 71: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 71: 26, 27, 28, 38} 71: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 71: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 71: 30, 34, 38, 39, 40} 71: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 71: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 71: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 71: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 71: 40} 71: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 71: 34, 35, 36, 37, 38, 39, 40} 71: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 71: 36, 37, 38} 71: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 71: 36, 37, 38} 71: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 71: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 71: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 71: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 71: 36, 37, 38} 71: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 71: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 71: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 71: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 71: 40, 41, 42, 43, 44, 58} 71: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 71: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 71: 45, 46, 47, 58, 59, 60} 71: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 71: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 71: 48, 50, 58, 59, 60, 61, 62} 71: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 71: 60} 71: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 71: 50, 51, 52, 54, 58, 59, 60} 71: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 71: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 71: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 71: 52, 53, 54, 55, 56, 58} 71: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 71: 54, 56, 57} 71: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 71: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 71: 55, 56, 57} 71: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 71: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 71: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 71: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 71: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 71: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 71: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 71: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 71: 60, 61, 62, 63, 64, 65} 71: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 71: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 71: 65, 66, 67} 71: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 71: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 71: 68, 69} 71: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 71: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 71: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71: 70, 71, 89} 71: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 71: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 71: 72, 73, 74, 89, 90, 91} 71: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 71: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 71: 75, 76, 77, 89, 90, 91, 92, 93} 71: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 71: 91} 71: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 71: 77, 78, 79, 80, 89, 90, 91} 71: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 71: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 71: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 71: 79, 80, 81, 82, 89} 71: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 71: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 71: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 71: 81, 82, 83, 86} 71: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 71: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 71: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 71: 84, 85, 86, 87, 88} 71: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 71: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 71: 87, 88} 71: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 71: excls[84][num=6]={80, 82, 83, 84, 85, 86} 71: excls[85][num=6]={80, 82, 83, 84, 85, 86} 71: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 71: excls[87][num=6]={80, 82, 83, 86, 87, 88} 71: excls[88][num=6]={80, 82, 83, 86, 87, 88} 71: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 71: 91, 92, 93, 94, 95, 100} 71: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 71: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 71: 96, 97, 98, 100, 101, 102} 71: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 71: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 71: 99, 100, 101, 102, 103, 104} 71: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 71: 102} 71: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 71: 101, 102} 71: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 71: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 71: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 71: excls[99][num=6]={93, 95, 96, 97, 98, 99} 71: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 71: 102, 103, 104, 105, 106, 115} 71: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 71: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 71: 106, 107, 108, 109, 115, 116, 117} 71: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 71: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 71: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 71: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 71: 115, 116, 117} 71: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 71: 110, 111, 112, 113, 114, 115, 116, 117} 71: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 71: 112, 115} 71: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 71: 112, 115} 71: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 71: 112, 113, 114, 115} 71: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 71: 114} 71: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 71: 114} 71: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 71: 114} 71: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 71: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 71: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 71: 115, 116, 117, 118, 119, 120, 121, 134} 71: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 71: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 71: 120, 121, 122, 123, 124, 134, 135, 136} 71: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 71: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 71: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 71: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 71: 134, 135, 136} 71: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 71: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 71: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 71: 130, 134} 71: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 71: 130, 134} 71: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 71: 127, 128, 129, 130, 131, 132, 133, 134} 71: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 71: 129, 130, 131, 132, 133} 71: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 71: 129, 130, 131, 132, 133} 71: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 71: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 71: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 71: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 71: 129, 130, 131, 132, 133} 71: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 71: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 71: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 71: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 71: 134, 135, 136, 137, 138, 139, 140, 144} 71: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 71: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 71: 139, 140, 141, 142, 143, 144, 145, 146} 71: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 71: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 71: 142, 143, 144, 145, 146, 147, 148} 71: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 71: 144, 145, 146} 71: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 71: 144, 145, 146} 71: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 71: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 71: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 71: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 71: 144, 145, 146, 147, 148, 149, 150, 154} 71: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 71: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 71: 149, 150, 151, 152, 153, 154, 155} 71: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 71: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 71: 152, 153, 154, 155} 71: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 71: 154, 155} 71: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 71: 154, 155} 71: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 71: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 71: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 71: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 71: 154, 155} 71: excls[155][num=6]={146, 148, 149, 150, 154, 155} 71: Bond: 71: nr: 468 71: iatoms: 71: 0 type=100 (BONDS) 0 1 71: 1 type=100 (BONDS) 0 2 71: 2 type=100 (BONDS) 0 3 71: 3 type=101 (BONDS) 0 4 71: 4 type=102 (BONDS) 4 5 71: 5 type=103 (BONDS) 4 6 71: 6 type=104 (BONDS) 4 22 71: 7 type=102 (BONDS) 6 7 71: 8 type=102 (BONDS) 6 8 71: 9 type=103 (BONDS) 6 9 71: 10 type=102 (BONDS) 9 10 71: 11 type=102 (BONDS) 9 11 71: 12 type=103 (BONDS) 9 12 71: 13 type=102 (BONDS) 12 13 71: 14 type=102 (BONDS) 12 14 71: 15 type=103 (BONDS) 12 15 71: 16 type=102 (BONDS) 15 16 71: 17 type=102 (BONDS) 15 17 71: 18 type=101 (BONDS) 15 18 71: 19 type=100 (BONDS) 18 19 71: 20 type=100 (BONDS) 18 20 71: 21 type=100 (BONDS) 18 21 71: 22 type=105 (BONDS) 22 23 71: 23 type=106 (BONDS) 22 24 71: 24 type=100 (BONDS) 24 25 71: 25 type=107 (BONDS) 24 26 71: 26 type=102 (BONDS) 26 27 71: 27 type=103 (BONDS) 26 28 71: 28 type=104 (BONDS) 26 38 71: 29 type=102 (BONDS) 28 29 71: 30 type=103 (BONDS) 28 30 71: 31 type=103 (BONDS) 28 34 71: 32 type=102 (BONDS) 30 31 71: 33 type=102 (BONDS) 30 32 71: 34 type=102 (BONDS) 30 33 71: 35 type=102 (BONDS) 34 35 71: 36 type=102 (BONDS) 34 36 71: 37 type=102 (BONDS) 34 37 71: 38 type=105 (BONDS) 38 39 71: 39 type=106 (BONDS) 38 40 71: 40 type=100 (BONDS) 40 41 71: 41 type=107 (BONDS) 40 42 71: 42 type=102 (BONDS) 42 43 71: 43 type=103 (BONDS) 42 44 71: 44 type=104 (BONDS) 42 58 71: 45 type=102 (BONDS) 44 45 71: 46 type=102 (BONDS) 44 46 71: 47 type=108 (BONDS) 44 47 71: 48 type=109 (BONDS) 47 48 71: 49 type=109 (BONDS) 47 50 71: 50 type=110 (BONDS) 48 49 71: 51 type=109 (BONDS) 48 52 71: 52 type=110 (BONDS) 50 51 71: 53 type=109 (BONDS) 50 54 71: 54 type=110 (BONDS) 52 53 71: 55 type=109 (BONDS) 52 56 71: 56 type=110 (BONDS) 54 55 71: 57 type=109 (BONDS) 54 56 71: 58 type=110 (BONDS) 56 57 71: 59 type=105 (BONDS) 58 59 71: 60 type=106 (BONDS) 58 60 71: 61 type=100 (BONDS) 60 61 71: 62 type=107 (BONDS) 60 62 71: 63 type=102 (BONDS) 62 63 71: 64 type=102 (BONDS) 62 64 71: 65 type=104 (BONDS) 62 65 71: 66 type=105 (BONDS) 65 66 71: 67 type=106 (BONDS) 65 67 71: 68 type=100 (BONDS) 67 68 71: 69 type=107 (BONDS) 67 69 71: 70 type=102 (BONDS) 69 70 71: 71 type=103 (BONDS) 69 71 71: 72 type=104 (BONDS) 69 89 71: 73 type=102 (BONDS) 71 72 71: 74 type=102 (BONDS) 71 73 71: 75 type=103 (BONDS) 71 74 71: 76 type=102 (BONDS) 74 75 71: 77 type=102 (BONDS) 74 76 71: 78 type=103 (BONDS) 74 77 71: 79 type=102 (BONDS) 77 78 71: 80 type=102 (BONDS) 77 79 71: 81 type=111 (BONDS) 77 80 71: 82 type=100 (BONDS) 80 81 71: 83 type=112 (BONDS) 80 82 71: 84 type=112 (BONDS) 82 83 71: 85 type=112 (BONDS) 82 86 71: 86 type=100 (BONDS) 83 84 71: 87 type=100 (BONDS) 83 85 71: 88 type=100 (BONDS) 86 87 71: 89 type=100 (BONDS) 86 88 71: 90 type=105 (BONDS) 89 90 71: 91 type=106 (BONDS) 89 91 71: 92 type=100 (BONDS) 91 92 71: 93 type=107 (BONDS) 91 93 71: 94 type=102 (BONDS) 93 94 71: 95 type=103 (BONDS) 93 95 71: 96 type=104 (BONDS) 93 100 71: 97 type=102 (BONDS) 95 96 71: 98 type=102 (BONDS) 95 97 71: 99 type=113 (BONDS) 95 98 71: 100 type=114 (BONDS) 98 99 71: 101 type=105 (BONDS) 100 101 71: 102 type=106 (BONDS) 100 102 71: 103 type=100 (BONDS) 102 103 71: 104 type=107 (BONDS) 102 104 71: 105 type=102 (BONDS) 104 105 71: 106 type=103 (BONDS) 104 106 71: 107 type=104 (BONDS) 104 115 71: 108 type=102 (BONDS) 106 107 71: 109 type=102 (BONDS) 106 108 71: 110 type=103 (BONDS) 106 109 71: 111 type=102 (BONDS) 109 110 71: 112 type=102 (BONDS) 109 111 71: 113 type=104 (BONDS) 109 112 71: 114 type=115 (BONDS) 112 113 71: 115 type=115 (BONDS) 112 114 71: 116 type=105 (BONDS) 115 116 71: 117 type=106 (BONDS) 115 117 71: 118 type=100 (BONDS) 117 118 71: 119 type=107 (BONDS) 117 119 71: 120 type=102 (BONDS) 119 120 71: 121 type=103 (BONDS) 119 121 71: 122 type=104 (BONDS) 119 134 71: 123 type=102 (BONDS) 121 122 71: 124 type=102 (BONDS) 121 123 71: 125 type=103 (BONDS) 121 124 71: 126 type=102 (BONDS) 124 125 71: 127 type=103 (BONDS) 124 126 71: 128 type=103 (BONDS) 124 130 71: 129 type=102 (BONDS) 126 127 71: 130 type=102 (BONDS) 126 128 71: 131 type=102 (BONDS) 126 129 71: 132 type=102 (BONDS) 130 131 71: 133 type=102 (BONDS) 130 132 71: 134 type=102 (BONDS) 130 133 71: 135 type=105 (BONDS) 134 135 71: 136 type=106 (BONDS) 134 136 71: 137 type=100 (BONDS) 136 137 71: 138 type=107 (BONDS) 136 138 71: 139 type=102 (BONDS) 138 139 71: 140 type=103 (BONDS) 138 140 71: 141 type=104 (BONDS) 138 144 71: 142 type=102 (BONDS) 140 141 71: 143 type=102 (BONDS) 140 142 71: 144 type=102 (BONDS) 140 143 71: 145 type=105 (BONDS) 144 145 71: 146 type=106 (BONDS) 144 146 71: 147 type=100 (BONDS) 146 147 71: 148 type=107 (BONDS) 146 148 71: 149 type=102 (BONDS) 148 149 71: 150 type=103 (BONDS) 148 150 71: 151 type=104 (BONDS) 148 154 71: 152 type=102 (BONDS) 150 151 71: 153 type=102 (BONDS) 150 152 71: 154 type=102 (BONDS) 150 153 71: 155 type=105 (BONDS) 154 155 71: G96Bond: 71: nr: 0 71: Morse: 71: nr: 0 71: Cubic Bonds: 71: nr: 0 71: Connect Bonds: 71: nr: 0 71: Harmonic Pot.: 71: nr: 0 71: FENE Bonds: 71: nr: 0 71: Tab. Bonds: 71: nr: 0 71: Tab. Bonds NC: 71: nr: 0 71: Restraint Pot.: 71: nr: 0 71: Angle: 71: nr: 1124 71: iatoms: 71: 0 type=116 (ANGLES) 1 0 2 71: 1 type=116 (ANGLES) 1 0 3 71: 2 type=116 (ANGLES) 1 0 4 71: 3 type=116 (ANGLES) 2 0 3 71: 4 type=116 (ANGLES) 2 0 4 71: 5 type=116 (ANGLES) 3 0 4 71: 6 type=116 (ANGLES) 0 4 5 71: 7 type=117 (ANGLES) 0 4 6 71: 8 type=117 (ANGLES) 0 4 22 71: 9 type=118 (ANGLES) 5 4 6 71: 10 type=116 (ANGLES) 5 4 22 71: 11 type=119 (ANGLES) 6 4 22 71: 12 type=118 (ANGLES) 4 6 7 71: 13 type=118 (ANGLES) 4 6 8 71: 14 type=120 (ANGLES) 4 6 9 71: 15 type=121 (ANGLES) 7 6 8 71: 16 type=118 (ANGLES) 7 6 9 71: 17 type=118 (ANGLES) 8 6 9 71: 18 type=118 (ANGLES) 6 9 10 71: 19 type=118 (ANGLES) 6 9 11 71: 20 type=120 (ANGLES) 6 9 12 71: 21 type=121 (ANGLES) 10 9 11 71: 22 type=118 (ANGLES) 10 9 12 71: 23 type=118 (ANGLES) 11 9 12 71: 24 type=118 (ANGLES) 9 12 13 71: 25 type=118 (ANGLES) 9 12 14 71: 26 type=120 (ANGLES) 9 12 15 71: 27 type=121 (ANGLES) 13 12 14 71: 28 type=118 (ANGLES) 13 12 15 71: 29 type=118 (ANGLES) 14 12 15 71: 30 type=118 (ANGLES) 12 15 16 71: 31 type=118 (ANGLES) 12 15 17 71: 32 type=117 (ANGLES) 12 15 18 71: 33 type=121 (ANGLES) 16 15 17 71: 34 type=116 (ANGLES) 16 15 18 71: 35 type=116 (ANGLES) 17 15 18 71: 36 type=116 (ANGLES) 15 18 19 71: 37 type=116 (ANGLES) 15 18 20 71: 38 type=116 (ANGLES) 15 18 21 71: 39 type=116 (ANGLES) 19 18 20 71: 40 type=116 (ANGLES) 19 18 21 71: 41 type=116 (ANGLES) 20 18 21 71: 42 type=122 (ANGLES) 4 22 23 71: 43 type=123 (ANGLES) 4 22 24 71: 44 type=124 (ANGLES) 23 22 24 71: 45 type=125 (ANGLES) 22 24 25 71: 46 type=126 (ANGLES) 22 24 26 71: 47 type=127 (ANGLES) 25 24 26 71: 48 type=116 (ANGLES) 24 26 27 71: 49 type=128 (ANGLES) 24 26 28 71: 50 type=129 (ANGLES) 24 26 38 71: 51 type=118 (ANGLES) 27 26 28 71: 52 type=116 (ANGLES) 27 26 38 71: 53 type=119 (ANGLES) 28 26 38 71: 54 type=118 (ANGLES) 26 28 29 71: 55 type=120 (ANGLES) 26 28 30 71: 56 type=120 (ANGLES) 26 28 34 71: 57 type=118 (ANGLES) 29 28 30 71: 58 type=118 (ANGLES) 29 28 34 71: 59 type=120 (ANGLES) 30 28 34 71: 60 type=118 (ANGLES) 28 30 31 71: 61 type=118 (ANGLES) 28 30 32 71: 62 type=118 (ANGLES) 28 30 33 71: 63 type=121 (ANGLES) 31 30 32 71: 64 type=121 (ANGLES) 31 30 33 71: 65 type=121 (ANGLES) 32 30 33 71: 66 type=118 (ANGLES) 28 34 35 71: 67 type=118 (ANGLES) 28 34 36 71: 68 type=118 (ANGLES) 28 34 37 71: 69 type=121 (ANGLES) 35 34 36 71: 70 type=121 (ANGLES) 35 34 37 71: 71 type=121 (ANGLES) 36 34 37 71: 72 type=122 (ANGLES) 26 38 39 71: 73 type=123 (ANGLES) 26 38 40 71: 74 type=124 (ANGLES) 39 38 40 71: 75 type=125 (ANGLES) 38 40 41 71: 76 type=126 (ANGLES) 38 40 42 71: 77 type=127 (ANGLES) 41 40 42 71: 78 type=116 (ANGLES) 40 42 43 71: 79 type=128 (ANGLES) 40 42 44 71: 80 type=129 (ANGLES) 40 42 58 71: 81 type=118 (ANGLES) 43 42 44 71: 82 type=116 (ANGLES) 43 42 58 71: 83 type=119 (ANGLES) 44 42 58 71: 84 type=118 (ANGLES) 42 44 45 71: 85 type=118 (ANGLES) 42 44 46 71: 86 type=130 (ANGLES) 42 44 47 71: 87 type=121 (ANGLES) 45 44 46 71: 88 type=116 (ANGLES) 45 44 47 71: 89 type=116 (ANGLES) 46 44 47 71: 90 type=131 (ANGLES) 44 47 48 71: 91 type=131 (ANGLES) 44 47 50 71: 92 type=132 (ANGLES) 48 47 50 71: 93 type=133 (ANGLES) 47 48 49 71: 94 type=132 (ANGLES) 47 48 52 71: 95 type=133 (ANGLES) 49 48 52 71: 96 type=133 (ANGLES) 47 50 51 71: 97 type=132 (ANGLES) 47 50 54 71: 98 type=133 (ANGLES) 51 50 54 71: 99 type=133 (ANGLES) 48 52 53 71: 100 type=132 (ANGLES) 48 52 56 71: 101 type=133 (ANGLES) 53 52 56 71: 102 type=133 (ANGLES) 50 54 55 71: 103 type=132 (ANGLES) 50 54 56 71: 104 type=133 (ANGLES) 55 54 56 71: 105 type=132 (ANGLES) 52 56 54 71: 106 type=133 (ANGLES) 52 56 57 71: 107 type=133 (ANGLES) 54 56 57 71: 108 type=122 (ANGLES) 42 58 59 71: 109 type=123 (ANGLES) 42 58 60 71: 110 type=124 (ANGLES) 59 58 60 71: 111 type=125 (ANGLES) 58 60 61 71: 112 type=126 (ANGLES) 58 60 62 71: 113 type=127 (ANGLES) 61 60 62 71: 114 type=116 (ANGLES) 60 62 63 71: 115 type=116 (ANGLES) 60 62 64 71: 116 type=129 (ANGLES) 60 62 65 71: 117 type=121 (ANGLES) 63 62 64 71: 118 type=116 (ANGLES) 63 62 65 71: 119 type=116 (ANGLES) 64 62 65 71: 120 type=122 (ANGLES) 62 65 66 71: 121 type=123 (ANGLES) 62 65 67 71: 122 type=124 (ANGLES) 66 65 67 71: 123 type=125 (ANGLES) 65 67 68 71: 124 type=126 (ANGLES) 65 67 69 71: 125 type=127 (ANGLES) 68 67 69 71: 126 type=116 (ANGLES) 67 69 70 71: 127 type=128 (ANGLES) 67 69 71 71: 128 type=129 (ANGLES) 67 69 89 71: 129 type=118 (ANGLES) 70 69 71 71: 130 type=116 (ANGLES) 70 69 89 71: 131 type=119 (ANGLES) 71 69 89 71: 132 type=118 (ANGLES) 69 71 72 71: 133 type=118 (ANGLES) 69 71 73 71: 134 type=120 (ANGLES) 69 71 74 71: 135 type=121 (ANGLES) 72 71 73 71: 136 type=118 (ANGLES) 72 71 74 71: 137 type=118 (ANGLES) 73 71 74 71: 138 type=118 (ANGLES) 71 74 75 71: 139 type=118 (ANGLES) 71 74 76 71: 140 type=120 (ANGLES) 71 74 77 71: 141 type=121 (ANGLES) 75 74 76 71: 142 type=118 (ANGLES) 75 74 77 71: 143 type=118 (ANGLES) 76 74 77 71: 144 type=118 (ANGLES) 74 77 78 71: 145 type=118 (ANGLES) 74 77 79 71: 146 type=117 (ANGLES) 74 77 80 71: 147 type=121 (ANGLES) 78 77 79 71: 148 type=116 (ANGLES) 78 77 80 71: 149 type=116 (ANGLES) 79 77 80 71: 150 type=134 (ANGLES) 77 80 81 71: 151 type=135 (ANGLES) 77 80 82 71: 152 type=133 (ANGLES) 81 80 82 71: 153 type=131 (ANGLES) 80 82 83 71: 154 type=131 (ANGLES) 80 82 86 71: 155 type=131 (ANGLES) 83 82 86 71: 156 type=133 (ANGLES) 82 83 84 71: 157 type=133 (ANGLES) 82 83 85 71: 158 type=133 (ANGLES) 84 83 85 71: 159 type=133 (ANGLES) 82 86 87 71: 160 type=133 (ANGLES) 82 86 88 71: 161 type=133 (ANGLES) 87 86 88 71: 162 type=122 (ANGLES) 69 89 90 71: 163 type=123 (ANGLES) 69 89 91 71: 164 type=124 (ANGLES) 90 89 91 71: 165 type=125 (ANGLES) 89 91 92 71: 166 type=126 (ANGLES) 89 91 93 71: 167 type=127 (ANGLES) 92 91 93 71: 168 type=116 (ANGLES) 91 93 94 71: 169 type=128 (ANGLES) 91 93 95 71: 170 type=129 (ANGLES) 91 93 100 71: 171 type=118 (ANGLES) 94 93 95 71: 172 type=116 (ANGLES) 94 93 100 71: 173 type=119 (ANGLES) 95 93 100 71: 174 type=118 (ANGLES) 93 95 96 71: 175 type=118 (ANGLES) 93 95 97 71: 176 type=136 (ANGLES) 93 95 98 71: 177 type=121 (ANGLES) 96 95 97 71: 178 type=116 (ANGLES) 96 95 98 71: 179 type=116 (ANGLES) 97 95 98 71: 180 type=137 (ANGLES) 95 98 99 71: 181 type=122 (ANGLES) 93 100 101 71: 182 type=123 (ANGLES) 93 100 102 71: 183 type=124 (ANGLES) 101 100 102 71: 184 type=125 (ANGLES) 100 102 103 71: 185 type=126 (ANGLES) 100 102 104 71: 186 type=127 (ANGLES) 103 102 104 71: 187 type=116 (ANGLES) 102 104 105 71: 188 type=128 (ANGLES) 102 104 106 71: 189 type=129 (ANGLES) 102 104 115 71: 190 type=118 (ANGLES) 105 104 106 71: 191 type=116 (ANGLES) 105 104 115 71: 192 type=119 (ANGLES) 106 104 115 71: 193 type=118 (ANGLES) 104 106 107 71: 194 type=118 (ANGLES) 104 106 108 71: 195 type=120 (ANGLES) 104 106 109 71: 196 type=121 (ANGLES) 107 106 108 71: 197 type=118 (ANGLES) 107 106 109 71: 198 type=118 (ANGLES) 108 106 109 71: 199 type=118 (ANGLES) 106 109 110 71: 200 type=118 (ANGLES) 106 109 111 71: 201 type=119 (ANGLES) 106 109 112 71: 202 type=121 (ANGLES) 110 109 111 71: 203 type=116 (ANGLES) 110 109 112 71: 204 type=116 (ANGLES) 111 109 112 71: 205 type=138 (ANGLES) 109 112 113 71: 206 type=138 (ANGLES) 109 112 114 71: 207 type=139 (ANGLES) 113 112 114 71: 208 type=122 (ANGLES) 104 115 116 71: 209 type=123 (ANGLES) 104 115 117 71: 210 type=124 (ANGLES) 116 115 117 71: 211 type=125 (ANGLES) 115 117 118 71: 212 type=126 (ANGLES) 115 117 119 71: 213 type=127 (ANGLES) 118 117 119 71: 214 type=116 (ANGLES) 117 119 120 71: 215 type=128 (ANGLES) 117 119 121 71: 216 type=129 (ANGLES) 117 119 134 71: 217 type=118 (ANGLES) 120 119 121 71: 218 type=116 (ANGLES) 120 119 134 71: 219 type=119 (ANGLES) 121 119 134 71: 220 type=118 (ANGLES) 119 121 122 71: 221 type=118 (ANGLES) 119 121 123 71: 222 type=120 (ANGLES) 119 121 124 71: 223 type=121 (ANGLES) 122 121 123 71: 224 type=118 (ANGLES) 122 121 124 71: 225 type=118 (ANGLES) 123 121 124 71: 226 type=118 (ANGLES) 121 124 125 71: 227 type=120 (ANGLES) 121 124 126 71: 228 type=120 (ANGLES) 121 124 130 71: 229 type=118 (ANGLES) 125 124 126 71: 230 type=118 (ANGLES) 125 124 130 71: 231 type=120 (ANGLES) 126 124 130 71: 232 type=118 (ANGLES) 124 126 127 71: 233 type=118 (ANGLES) 124 126 128 71: 234 type=118 (ANGLES) 124 126 129 71: 235 type=121 (ANGLES) 127 126 128 71: 236 type=121 (ANGLES) 127 126 129 71: 237 type=121 (ANGLES) 128 126 129 71: 238 type=118 (ANGLES) 124 130 131 71: 239 type=118 (ANGLES) 124 130 132 71: 240 type=118 (ANGLES) 124 130 133 71: 241 type=121 (ANGLES) 131 130 132 71: 242 type=121 (ANGLES) 131 130 133 71: 243 type=121 (ANGLES) 132 130 133 71: 244 type=122 (ANGLES) 119 134 135 71: 245 type=123 (ANGLES) 119 134 136 71: 246 type=124 (ANGLES) 135 134 136 71: 247 type=125 (ANGLES) 134 136 137 71: 248 type=126 (ANGLES) 134 136 138 71: 249 type=127 (ANGLES) 137 136 138 71: 250 type=116 (ANGLES) 136 138 139 71: 251 type=128 (ANGLES) 136 138 140 71: 252 type=129 (ANGLES) 136 138 144 71: 253 type=118 (ANGLES) 139 138 140 71: 254 type=116 (ANGLES) 139 138 144 71: 255 type=119 (ANGLES) 140 138 144 71: 256 type=118 (ANGLES) 138 140 141 71: 257 type=118 (ANGLES) 138 140 142 71: 258 type=118 (ANGLES) 138 140 143 71: 259 type=121 (ANGLES) 141 140 142 71: 260 type=121 (ANGLES) 141 140 143 71: 261 type=121 (ANGLES) 142 140 143 71: 262 type=122 (ANGLES) 138 144 145 71: 263 type=123 (ANGLES) 138 144 146 71: 264 type=124 (ANGLES) 145 144 146 71: 265 type=125 (ANGLES) 144 146 147 71: 266 type=126 (ANGLES) 144 146 148 71: 267 type=127 (ANGLES) 147 146 148 71: 268 type=116 (ANGLES) 146 148 149 71: 269 type=128 (ANGLES) 146 148 150 71: 270 type=129 (ANGLES) 146 148 154 71: 271 type=118 (ANGLES) 149 148 150 71: 272 type=116 (ANGLES) 149 148 154 71: 273 type=119 (ANGLES) 150 148 154 71: 274 type=118 (ANGLES) 148 150 151 71: 275 type=118 (ANGLES) 148 150 152 71: 276 type=118 (ANGLES) 148 150 153 71: 277 type=121 (ANGLES) 151 150 152 71: 278 type=121 (ANGLES) 151 150 153 71: 279 type=121 (ANGLES) 152 150 153 71: 280 type=122 (ANGLES) 148 154 155 71: G96Angle: 71: nr: 0 71: Restr. Angles: 71: nr: 0 71: Lin. Angle: 71: nr: 0 71: Bond-Cross: 71: nr: 0 71: BA-Cross: 71: nr: 0 71: U-B: 71: nr: 0 71: Quartic Angles: 71: nr: 0 71: Tab. Angles: 71: nr: 0 71: Proper Dih.: 71: nr: 145 71: iatoms: 71: 0 type=140 (PDIHS) 4 24 22 23 71: 1 type=141 (PDIHS) 22 26 24 25 71: 2 type=140 (PDIHS) 26 40 38 39 71: 3 type=141 (PDIHS) 38 42 40 41 71: 4 type=140 (PDIHS) 42 60 58 59 71: 5 type=142 (PDIHS) 44 47 50 48 71: 6 type=142 (PDIHS) 47 52 48 49 71: 7 type=142 (PDIHS) 47 54 50 51 71: 8 type=142 (PDIHS) 48 56 52 53 71: 9 type=142 (PDIHS) 50 56 54 55 71: 10 type=142 (PDIHS) 52 54 56 57 71: 11 type=141 (PDIHS) 58 62 60 61 71: 12 type=140 (PDIHS) 62 67 65 66 71: 13 type=141 (PDIHS) 65 69 67 68 71: 14 type=140 (PDIHS) 69 91 89 90 71: 15 type=141 (PDIHS) 77 82 80 81 71: 16 type=140 (PDIHS) 80 83 82 86 71: 17 type=141 (PDIHS) 82 84 83 85 71: 18 type=141 (PDIHS) 82 87 86 88 71: 19 type=141 (PDIHS) 89 93 91 92 71: 20 type=140 (PDIHS) 93 102 100 101 71: 21 type=141 (PDIHS) 100 104 102 103 71: 22 type=140 (PDIHS) 104 117 115 116 71: 23 type=140 (PDIHS) 109 113 112 114 71: 24 type=141 (PDIHS) 115 119 117 118 71: 25 type=140 (PDIHS) 119 136 134 135 71: 26 type=141 (PDIHS) 134 138 136 137 71: 27 type=140 (PDIHS) 138 146 144 145 71: 28 type=141 (PDIHS) 144 148 146 147 71: Ryckaert-Bell.: 71: nr: 1565 71: iatoms: 71: 0 type=143 (RBDIHS) 1 0 4 5 71: 1 type=144 (RBDIHS) 1 0 4 6 71: 2 type=144 (RBDIHS) 1 0 4 22 71: 3 type=143 (RBDIHS) 2 0 4 5 71: 4 type=144 (RBDIHS) 2 0 4 6 71: 5 type=144 (RBDIHS) 2 0 4 22 71: 6 type=143 (RBDIHS) 3 0 4 5 71: 7 type=144 (RBDIHS) 3 0 4 6 71: 8 type=144 (RBDIHS) 3 0 4 22 71: 9 type=145 (RBDIHS) 0 4 6 9 71: 10 type=146 (RBDIHS) 22 4 6 9 71: 11 type=147 (RBDIHS) 0 4 6 7 71: 12 type=147 (RBDIHS) 0 4 6 8 71: 13 type=148 (RBDIHS) 5 4 6 7 71: 14 type=148 (RBDIHS) 5 4 6 8 71: 15 type=148 (RBDIHS) 5 4 6 9 71: 16 type=149 (RBDIHS) 22 4 6 7 71: 17 type=149 (RBDIHS) 22 4 6 8 71: 18 type=150 (RBDIHS) 0 4 22 24 71: 19 type=151 (RBDIHS) 6 4 22 24 71: 20 type=148 (RBDIHS) 4 6 9 10 71: 21 type=148 (RBDIHS) 4 6 9 11 71: 22 type=152 (RBDIHS) 4 6 9 12 71: 23 type=148 (RBDIHS) 7 6 9 10 71: 24 type=148 (RBDIHS) 7 6 9 11 71: 25 type=148 (RBDIHS) 7 6 9 12 71: 26 type=148 (RBDIHS) 8 6 9 10 71: 27 type=148 (RBDIHS) 8 6 9 11 71: 28 type=148 (RBDIHS) 8 6 9 12 71: 29 type=148 (RBDIHS) 6 9 12 13 71: 30 type=148 (RBDIHS) 6 9 12 14 71: 31 type=152 (RBDIHS) 6 9 12 15 71: 32 type=148 (RBDIHS) 10 9 12 13 71: 33 type=148 (RBDIHS) 10 9 12 14 71: 34 type=148 (RBDIHS) 10 9 12 15 71: 35 type=148 (RBDIHS) 11 9 12 13 71: 36 type=148 (RBDIHS) 11 9 12 14 71: 37 type=148 (RBDIHS) 11 9 12 15 71: 38 type=148 (RBDIHS) 9 12 15 16 71: 39 type=148 (RBDIHS) 9 12 15 17 71: 40 type=153 (RBDIHS) 9 12 15 18 71: 41 type=148 (RBDIHS) 13 12 15 16 71: 42 type=148 (RBDIHS) 13 12 15 17 71: 43 type=154 (RBDIHS) 13 12 15 18 71: 44 type=148 (RBDIHS) 14 12 15 16 71: 45 type=148 (RBDIHS) 14 12 15 17 71: 46 type=154 (RBDIHS) 14 12 15 18 71: 47 type=144 (RBDIHS) 12 15 18 19 71: 48 type=144 (RBDIHS) 12 15 18 20 71: 49 type=144 (RBDIHS) 12 15 18 21 71: 50 type=143 (RBDIHS) 16 15 18 19 71: 51 type=143 (RBDIHS) 16 15 18 20 71: 52 type=143 (RBDIHS) 16 15 18 21 71: 53 type=143 (RBDIHS) 17 15 18 19 71: 54 type=143 (RBDIHS) 17 15 18 20 71: 55 type=143 (RBDIHS) 17 15 18 21 71: 56 type=155 (RBDIHS) 4 22 24 25 71: 57 type=156 (RBDIHS) 4 22 24 26 71: 58 type=155 (RBDIHS) 23 22 24 25 71: 59 type=157 (RBDIHS) 23 22 24 26 71: 60 type=158 (RBDIHS) 22 24 26 28 71: 61 type=159 (RBDIHS) 22 24 26 38 71: 62 type=160 (RBDIHS) 24 26 28 30 71: 63 type=160 (RBDIHS) 24 26 28 34 71: 64 type=161 (RBDIHS) 38 26 28 30 71: 65 type=161 (RBDIHS) 38 26 28 34 71: 66 type=147 (RBDIHS) 24 26 28 29 71: 67 type=148 (RBDIHS) 27 26 28 29 71: 68 type=148 (RBDIHS) 27 26 28 30 71: 69 type=148 (RBDIHS) 27 26 28 34 71: 70 type=149 (RBDIHS) 38 26 28 29 71: 71 type=150 (RBDIHS) 24 26 38 40 71: 72 type=151 (RBDIHS) 28 26 38 40 71: 73 type=148 (RBDIHS) 26 28 30 31 71: 74 type=148 (RBDIHS) 26 28 30 32 71: 75 type=148 (RBDIHS) 26 28 30 33 71: 76 type=148 (RBDIHS) 29 28 30 31 71: 77 type=148 (RBDIHS) 29 28 30 32 71: 78 type=148 (RBDIHS) 29 28 30 33 71: 79 type=148 (RBDIHS) 34 28 30 31 71: 80 type=148 (RBDIHS) 34 28 30 32 71: 81 type=148 (RBDIHS) 34 28 30 33 71: 82 type=148 (RBDIHS) 26 28 34 35 71: 83 type=148 (RBDIHS) 26 28 34 36 71: 84 type=148 (RBDIHS) 26 28 34 37 71: 85 type=148 (RBDIHS) 29 28 34 35 71: 86 type=148 (RBDIHS) 29 28 34 36 71: 87 type=148 (RBDIHS) 29 28 34 37 71: 88 type=148 (RBDIHS) 30 28 34 35 71: 89 type=148 (RBDIHS) 30 28 34 36 71: 90 type=148 (RBDIHS) 30 28 34 37 71: 91 type=155 (RBDIHS) 26 38 40 41 71: 92 type=156 (RBDIHS) 26 38 40 42 71: 93 type=155 (RBDIHS) 39 38 40 41 71: 94 type=157 (RBDIHS) 39 38 40 42 71: 95 type=158 (RBDIHS) 38 40 42 44 71: 96 type=159 (RBDIHS) 38 40 42 58 71: 97 type=147 (RBDIHS) 40 42 44 45 71: 98 type=147 (RBDIHS) 40 42 44 46 71: 99 type=162 (RBDIHS) 40 42 44 47 71: 100 type=148 (RBDIHS) 43 42 44 45 71: 101 type=148 (RBDIHS) 43 42 44 46 71: 102 type=163 (RBDIHS) 43 42 44 47 71: 103 type=149 (RBDIHS) 58 42 44 45 71: 104 type=149 (RBDIHS) 58 42 44 46 71: 105 type=164 (RBDIHS) 58 42 44 47 71: 106 type=150 (RBDIHS) 40 42 58 60 71: 107 type=151 (RBDIHS) 44 42 58 60 71: 108 type=165 (RBDIHS) 44 47 48 49 71: 109 type=165 (RBDIHS) 44 47 48 52 71: 110 type=165 (RBDIHS) 50 47 48 49 71: 111 type=165 (RBDIHS) 50 47 48 52 71: 112 type=165 (RBDIHS) 44 47 50 51 71: 113 type=165 (RBDIHS) 44 47 50 54 71: 114 type=165 (RBDIHS) 48 47 50 51 71: 115 type=165 (RBDIHS) 48 47 50 54 71: 116 type=165 (RBDIHS) 47 48 52 53 71: 117 type=165 (RBDIHS) 47 48 52 56 71: 118 type=165 (RBDIHS) 49 48 52 53 71: 119 type=165 (RBDIHS) 49 48 52 56 71: 120 type=165 (RBDIHS) 47 50 54 55 71: 121 type=165 (RBDIHS) 47 50 54 56 71: 122 type=165 (RBDIHS) 51 50 54 55 71: 123 type=165 (RBDIHS) 51 50 54 56 71: 124 type=165 (RBDIHS) 48 52 56 54 71: 125 type=165 (RBDIHS) 48 52 56 57 71: 126 type=165 (RBDIHS) 53 52 56 54 71: 127 type=165 (RBDIHS) 53 52 56 57 71: 128 type=165 (RBDIHS) 50 54 56 52 71: 129 type=165 (RBDIHS) 50 54 56 57 71: 130 type=165 (RBDIHS) 55 54 56 52 71: 131 type=165 (RBDIHS) 55 54 56 57 71: 132 type=155 (RBDIHS) 42 58 60 61 71: 133 type=156 (RBDIHS) 42 58 60 62 71: 134 type=155 (RBDIHS) 59 58 60 61 71: 135 type=157 (RBDIHS) 59 58 60 62 71: 136 type=159 (RBDIHS) 58 60 62 65 71: 137 type=150 (RBDIHS) 60 62 65 67 71: 138 type=155 (RBDIHS) 62 65 67 68 71: 139 type=156 (RBDIHS) 62 65 67 69 71: 140 type=155 (RBDIHS) 66 65 67 68 71: 141 type=157 (RBDIHS) 66 65 67 69 71: 142 type=158 (RBDIHS) 65 67 69 71 71: 143 type=159 (RBDIHS) 65 67 69 89 71: 144 type=166 (RBDIHS) 67 69 71 74 71: 145 type=167 (RBDIHS) 89 69 71 74 71: 146 type=147 (RBDIHS) 67 69 71 72 71: 147 type=147 (RBDIHS) 67 69 71 73 71: 148 type=148 (RBDIHS) 70 69 71 72 71: 149 type=148 (RBDIHS) 70 69 71 73 71: 150 type=148 (RBDIHS) 70 69 71 74 71: 151 type=149 (RBDIHS) 89 69 71 72 71: 152 type=149 (RBDIHS) 89 69 71 73 71: 153 type=150 (RBDIHS) 67 69 89 91 71: 154 type=151 (RBDIHS) 71 69 89 91 71: 155 type=148 (RBDIHS) 69 71 74 75 71: 156 type=148 (RBDIHS) 69 71 74 76 71: 157 type=152 (RBDIHS) 69 71 74 77 71: 158 type=148 (RBDIHS) 72 71 74 75 71: 159 type=148 (RBDIHS) 72 71 74 76 71: 160 type=148 (RBDIHS) 72 71 74 77 71: 161 type=148 (RBDIHS) 73 71 74 75 71: 162 type=148 (RBDIHS) 73 71 74 76 71: 163 type=148 (RBDIHS) 73 71 74 77 71: 164 type=148 (RBDIHS) 71 74 77 78 71: 165 type=148 (RBDIHS) 71 74 77 79 71: 166 type=153 (RBDIHS) 71 74 77 80 71: 167 type=148 (RBDIHS) 75 74 77 78 71: 168 type=148 (RBDIHS) 75 74 77 79 71: 169 type=168 (RBDIHS) 75 74 77 80 71: 170 type=148 (RBDIHS) 76 74 77 78 71: 171 type=148 (RBDIHS) 76 74 77 79 71: 172 type=168 (RBDIHS) 76 74 77 80 71: 173 type=169 (RBDIHS) 74 77 80 81 71: 174 type=170 (RBDIHS) 74 77 80 82 71: 175 type=171 (RBDIHS) 78 77 80 82 71: 176 type=171 (RBDIHS) 79 77 80 82 71: 177 type=172 (RBDIHS) 77 80 82 83 71: 178 type=172 (RBDIHS) 77 80 82 86 71: 179 type=173 (RBDIHS) 81 80 82 83 71: 180 type=173 (RBDIHS) 81 80 82 86 71: 181 type=173 (RBDIHS) 80 82 83 84 71: 182 type=173 (RBDIHS) 80 82 83 85 71: 183 type=173 (RBDIHS) 86 82 83 84 71: 184 type=173 (RBDIHS) 86 82 83 85 71: 185 type=173 (RBDIHS) 80 82 86 87 71: 186 type=173 (RBDIHS) 80 82 86 88 71: 187 type=173 (RBDIHS) 83 82 86 87 71: 188 type=173 (RBDIHS) 83 82 86 88 71: 189 type=155 (RBDIHS) 69 89 91 92 71: 190 type=156 (RBDIHS) 69 89 91 93 71: 191 type=155 (RBDIHS) 90 89 91 92 71: 192 type=157 (RBDIHS) 90 89 91 93 71: 193 type=158 (RBDIHS) 89 91 93 95 71: 194 type=159 (RBDIHS) 89 91 93 100 71: 195 type=174 (RBDIHS) 91 93 95 98 71: 196 type=175 (RBDIHS) 100 93 95 98 71: 197 type=147 (RBDIHS) 91 93 95 96 71: 198 type=147 (RBDIHS) 91 93 95 97 71: 199 type=148 (RBDIHS) 94 93 95 96 71: 200 type=148 (RBDIHS) 94 93 95 97 71: 201 type=176 (RBDIHS) 94 93 95 98 71: 202 type=149 (RBDIHS) 100 93 95 96 71: 203 type=149 (RBDIHS) 100 93 95 97 71: 204 type=150 (RBDIHS) 91 93 100 102 71: 205 type=151 (RBDIHS) 95 93 100 102 71: 206 type=177 (RBDIHS) 93 95 98 99 71: 207 type=178 (RBDIHS) 96 95 98 99 71: 208 type=178 (RBDIHS) 97 95 98 99 71: 209 type=155 (RBDIHS) 93 100 102 103 71: 210 type=156 (RBDIHS) 93 100 102 104 71: 211 type=155 (RBDIHS) 101 100 102 103 71: 212 type=157 (RBDIHS) 101 100 102 104 71: 213 type=158 (RBDIHS) 100 102 104 106 71: 214 type=159 (RBDIHS) 100 102 104 115 71: 215 type=179 (RBDIHS) 102 104 106 109 71: 216 type=180 (RBDIHS) 115 104 106 109 71: 217 type=147 (RBDIHS) 102 104 106 107 71: 218 type=147 (RBDIHS) 102 104 106 108 71: 219 type=148 (RBDIHS) 105 104 106 107 71: 220 type=148 (RBDIHS) 105 104 106 108 71: 221 type=148 (RBDIHS) 105 104 106 109 71: 222 type=149 (RBDIHS) 115 104 106 107 71: 223 type=149 (RBDIHS) 115 104 106 108 71: 224 type=150 (RBDIHS) 102 104 115 117 71: 225 type=151 (RBDIHS) 106 104 115 117 71: 226 type=148 (RBDIHS) 104 106 109 110 71: 227 type=148 (RBDIHS) 104 106 109 111 71: 228 type=181 (RBDIHS) 104 106 109 112 71: 229 type=148 (RBDIHS) 107 106 109 110 71: 230 type=148 (RBDIHS) 107 106 109 111 71: 231 type=182 (RBDIHS) 107 106 109 112 71: 232 type=148 (RBDIHS) 108 106 109 110 71: 233 type=148 (RBDIHS) 108 106 109 111 71: 234 type=182 (RBDIHS) 108 106 109 112 71: 235 type=183 (RBDIHS) 106 109 112 113 71: 236 type=183 (RBDIHS) 106 109 112 114 71: 237 type=155 (RBDIHS) 104 115 117 118 71: 238 type=156 (RBDIHS) 104 115 117 119 71: 239 type=155 (RBDIHS) 116 115 117 118 71: 240 type=157 (RBDIHS) 116 115 117 119 71: 241 type=158 (RBDIHS) 115 117 119 121 71: 242 type=159 (RBDIHS) 115 117 119 134 71: 243 type=184 (RBDIHS) 117 119 121 124 71: 244 type=185 (RBDIHS) 134 119 121 124 71: 245 type=147 (RBDIHS) 117 119 121 122 71: 246 type=147 (RBDIHS) 117 119 121 123 71: 247 type=148 (RBDIHS) 120 119 121 122 71: 248 type=148 (RBDIHS) 120 119 121 123 71: 249 type=148 (RBDIHS) 120 119 121 124 71: 250 type=149 (RBDIHS) 134 119 121 122 71: 251 type=149 (RBDIHS) 134 119 121 123 71: 252 type=150 (RBDIHS) 117 119 134 136 71: 253 type=151 (RBDIHS) 121 119 134 136 71: 254 type=148 (RBDIHS) 119 121 124 125 71: 255 type=152 (RBDIHS) 119 121 124 126 71: 256 type=152 (RBDIHS) 119 121 124 130 71: 257 type=148 (RBDIHS) 122 121 124 125 71: 258 type=148 (RBDIHS) 122 121 124 126 71: 259 type=148 (RBDIHS) 122 121 124 130 71: 260 type=148 (RBDIHS) 123 121 124 125 71: 261 type=148 (RBDIHS) 123 121 124 126 71: 262 type=148 (RBDIHS) 123 121 124 130 71: 263 type=148 (RBDIHS) 121 124 126 127 71: 264 type=148 (RBDIHS) 121 124 126 128 71: 265 type=148 (RBDIHS) 121 124 126 129 71: 266 type=148 (RBDIHS) 125 124 126 127 71: 267 type=148 (RBDIHS) 125 124 126 128 71: 268 type=148 (RBDIHS) 125 124 126 129 71: 269 type=148 (RBDIHS) 130 124 126 127 71: 270 type=148 (RBDIHS) 130 124 126 128 71: 271 type=148 (RBDIHS) 130 124 126 129 71: 272 type=148 (RBDIHS) 121 124 130 131 71: 273 type=148 (RBDIHS) 121 124 130 132 71: 274 type=148 (RBDIHS) 121 124 130 133 71: 275 type=148 (RBDIHS) 125 124 130 131 71: 276 type=148 (RBDIHS) 125 124 130 132 71: 277 type=148 (RBDIHS) 125 124 130 133 71: 278 type=148 (RBDIHS) 126 124 130 131 71: 279 type=148 (RBDIHS) 126 124 130 132 71: 280 type=148 (RBDIHS) 126 124 130 133 71: 281 type=155 (RBDIHS) 119 134 136 137 71: 282 type=156 (RBDIHS) 119 134 136 138 71: 283 type=155 (RBDIHS) 135 134 136 137 71: 284 type=157 (RBDIHS) 135 134 136 138 71: 285 type=158 (RBDIHS) 134 136 138 140 71: 286 type=159 (RBDIHS) 134 136 138 144 71: 287 type=147 (RBDIHS) 136 138 140 141 71: 288 type=147 (RBDIHS) 136 138 140 142 71: 289 type=147 (RBDIHS) 136 138 140 143 71: 290 type=148 (RBDIHS) 139 138 140 141 71: 291 type=148 (RBDIHS) 139 138 140 142 71: 292 type=148 (RBDIHS) 139 138 140 143 71: 293 type=149 (RBDIHS) 144 138 140 141 71: 294 type=149 (RBDIHS) 144 138 140 142 71: 295 type=149 (RBDIHS) 144 138 140 143 71: 296 type=150 (RBDIHS) 136 138 144 146 71: 297 type=151 (RBDIHS) 140 138 144 146 71: 298 type=155 (RBDIHS) 138 144 146 147 71: 299 type=156 (RBDIHS) 138 144 146 148 71: 300 type=155 (RBDIHS) 145 144 146 147 71: 301 type=157 (RBDIHS) 145 144 146 148 71: 302 type=158 (RBDIHS) 144 146 148 150 71: 303 type=159 (RBDIHS) 144 146 148 154 71: 304 type=147 (RBDIHS) 146 148 150 151 71: 305 type=147 (RBDIHS) 146 148 150 152 71: 306 type=147 (RBDIHS) 146 148 150 153 71: 307 type=148 (RBDIHS) 149 148 150 151 71: 308 type=148 (RBDIHS) 149 148 150 152 71: 309 type=148 (RBDIHS) 149 148 150 153 71: 310 type=149 (RBDIHS) 154 148 150 151 71: 311 type=149 (RBDIHS) 154 148 150 152 71: 312 type=149 (RBDIHS) 154 148 150 153 71: Restr. Dih.: 71: nr: 0 71: CBT Dih.: 71: nr: 0 71: Fourier Dih.: 71: nr: 0 71: Improper Dih.: 71: nr: 0 71: Per. Imp. Dih.: 71: nr: 0 71: Tab. Dih.: 71: nr: 0 71: CMAP Dih.: 71: nr: 0 71: GB 1-2 Pol.: 71: nr: 0 71: GB 1-3 Pol.: 71: nr: 0 71: GB 1-4 Pol.: 71: nr: 0 71: GB Polariz.: 71: nr: 0 71: Nonpolar Sol.: 71: nr: 0 71: LJ-14: 71: nr: 1197 71: iatoms: 71: 0 type=186 (LJ14) 0 7 71: 1 type=186 (LJ14) 0 8 71: 2 type=187 (LJ14) 0 9 71: 3 type=188 (LJ14) 0 23 71: 4 type=189 (LJ14) 0 24 71: 5 type=190 (LJ14) 1 5 71: 6 type=190 (LJ14) 1 6 71: 7 type=190 (LJ14) 1 22 71: 8 type=190 (LJ14) 2 5 71: 9 type=190 (LJ14) 2 6 71: 10 type=190 (LJ14) 2 22 71: 11 type=190 (LJ14) 3 5 71: 12 type=190 (LJ14) 3 6 71: 13 type=190 (LJ14) 3 22 71: 14 type=191 (LJ14) 4 10 71: 15 type=191 (LJ14) 4 11 71: 16 type=192 (LJ14) 4 12 71: 17 type=190 (LJ14) 4 25 71: 18 type=192 (LJ14) 4 26 71: 19 type=193 (LJ14) 5 7 71: 20 type=193 (LJ14) 5 8 71: 21 type=191 (LJ14) 5 9 71: 22 type=194 (LJ14) 5 23 71: 23 type=186 (LJ14) 5 24 71: 24 type=191 (LJ14) 6 13 71: 25 type=191 (LJ14) 6 14 71: 26 type=192 (LJ14) 6 15 71: 27 type=195 (LJ14) 6 23 71: 28 type=187 (LJ14) 6 24 71: 29 type=193 (LJ14) 7 10 71: 30 type=193 (LJ14) 7 11 71: 31 type=191 (LJ14) 7 12 71: 32 type=196 (LJ14) 7 22 71: 33 type=193 (LJ14) 8 10 71: 34 type=193 (LJ14) 8 11 71: 35 type=191 (LJ14) 8 12 71: 36 type=196 (LJ14) 8 22 71: 37 type=191 (LJ14) 9 16 71: 38 type=191 (LJ14) 9 17 71: 39 type=187 (LJ14) 9 18 71: 40 type=197 (LJ14) 9 22 71: 41 type=193 (LJ14) 10 13 71: 42 type=193 (LJ14) 10 14 71: 43 type=191 (LJ14) 10 15 71: 44 type=193 (LJ14) 11 13 71: 45 type=193 (LJ14) 11 14 71: 46 type=191 (LJ14) 11 15 71: 47 type=190 (LJ14) 12 19 71: 48 type=190 (LJ14) 12 20 71: 49 type=190 (LJ14) 12 21 71: 50 type=193 (LJ14) 13 16 71: 51 type=193 (LJ14) 13 17 71: 52 type=186 (LJ14) 13 18 71: 53 type=193 (LJ14) 14 16 71: 54 type=193 (LJ14) 14 17 71: 55 type=186 (LJ14) 14 18 71: 56 type=190 (LJ14) 16 19 71: 57 type=190 (LJ14) 16 20 71: 58 type=190 (LJ14) 16 21 71: 59 type=190 (LJ14) 17 19 71: 60 type=190 (LJ14) 17 20 71: 61 type=190 (LJ14) 17 21 71: 62 type=196 (LJ14) 22 27 71: 63 type=197 (LJ14) 22 28 71: 64 type=198 (LJ14) 22 38 71: 65 type=190 (LJ14) 23 25 71: 66 type=195 (LJ14) 23 26 71: 67 type=186 (LJ14) 24 29 71: 68 type=187 (LJ14) 24 30 71: 69 type=187 (LJ14) 24 34 71: 70 type=188 (LJ14) 24 39 71: 71 type=189 (LJ14) 24 40 71: 72 type=190 (LJ14) 25 27 71: 73 type=190 (LJ14) 25 28 71: 74 type=190 (LJ14) 25 38 71: 75 type=191 (LJ14) 26 31 71: 76 type=191 (LJ14) 26 32 71: 77 type=191 (LJ14) 26 33 71: 78 type=191 (LJ14) 26 35 71: 79 type=191 (LJ14) 26 36 71: 80 type=191 (LJ14) 26 37 71: 81 type=190 (LJ14) 26 41 71: 82 type=192 (LJ14) 26 42 71: 83 type=193 (LJ14) 27 29 71: 84 type=191 (LJ14) 27 30 71: 85 type=191 (LJ14) 27 34 71: 86 type=194 (LJ14) 27 39 71: 87 type=186 (LJ14) 27 40 71: 88 type=195 (LJ14) 28 39 71: 89 type=187 (LJ14) 28 40 71: 90 type=193 (LJ14) 29 31 71: 91 type=193 (LJ14) 29 32 71: 92 type=193 (LJ14) 29 33 71: 93 type=193 (LJ14) 29 35 71: 94 type=193 (LJ14) 29 36 71: 95 type=193 (LJ14) 29 37 71: 96 type=196 (LJ14) 29 38 71: 97 type=191 (LJ14) 30 35 71: 98 type=191 (LJ14) 30 36 71: 99 type=191 (LJ14) 30 37 71: 100 type=197 (LJ14) 30 38 71: 101 type=191 (LJ14) 31 34 71: 102 type=191 (LJ14) 32 34 71: 103 type=191 (LJ14) 33 34 71: 104 type=197 (LJ14) 34 38 71: 105 type=196 (LJ14) 38 43 71: 106 type=197 (LJ14) 38 44 71: 107 type=198 (LJ14) 38 58 71: 108 type=190 (LJ14) 39 41 71: 109 type=195 (LJ14) 39 42 71: 110 type=186 (LJ14) 40 45 71: 111 type=186 (LJ14) 40 46 71: 112 type=199 (LJ14) 40 47 71: 113 type=188 (LJ14) 40 59 71: 114 type=189 (LJ14) 40 60 71: 115 type=190 (LJ14) 41 43 71: 116 type=190 (LJ14) 41 44 71: 117 type=190 (LJ14) 41 58 71: 118 type=200 (LJ14) 42 48 71: 119 type=200 (LJ14) 42 50 71: 120 type=190 (LJ14) 42 61 71: 121 type=192 (LJ14) 42 62 71: 122 type=193 (LJ14) 43 45 71: 123 type=193 (LJ14) 43 46 71: 124 type=201 (LJ14) 43 47 71: 125 type=194 (LJ14) 43 59 71: 126 type=186 (LJ14) 43 60 71: 127 type=202 (LJ14) 44 49 71: 128 type=202 (LJ14) 44 51 71: 129 type=200 (LJ14) 44 52 71: 130 type=200 (LJ14) 44 54 71: 131 type=195 (LJ14) 44 59 71: 132 type=187 (LJ14) 44 60 71: 133 type=201 (LJ14) 45 48 71: 134 type=201 (LJ14) 45 50 71: 135 type=196 (LJ14) 45 58 71: 136 type=201 (LJ14) 46 48 71: 137 type=201 (LJ14) 46 50 71: 138 type=196 (LJ14) 46 58 71: 139 type=203 (LJ14) 47 53 71: 140 type=203 (LJ14) 47 55 71: 141 type=204 (LJ14) 47 56 71: 142 type=205 (LJ14) 47 58 71: 143 type=203 (LJ14) 48 51 71: 144 type=204 (LJ14) 48 54 71: 145 type=203 (LJ14) 48 57 71: 146 type=203 (LJ14) 49 50 71: 147 type=206 (LJ14) 49 53 71: 148 type=203 (LJ14) 49 56 71: 149 type=204 (LJ14) 50 52 71: 150 type=203 (LJ14) 50 57 71: 151 type=206 (LJ14) 51 55 71: 152 type=203 (LJ14) 51 56 71: 153 type=203 (LJ14) 52 55 71: 154 type=203 (LJ14) 53 54 71: 155 type=206 (LJ14) 53 57 71: 156 type=206 (LJ14) 55 57 71: 157 type=196 (LJ14) 58 63 71: 158 type=196 (LJ14) 58 64 71: 159 type=198 (LJ14) 58 65 71: 160 type=190 (LJ14) 59 61 71: 161 type=195 (LJ14) 59 62 71: 162 type=188 (LJ14) 60 66 71: 163 type=189 (LJ14) 60 67 71: 164 type=190 (LJ14) 61 63 71: 165 type=190 (LJ14) 61 64 71: 166 type=190 (LJ14) 61 65 71: 167 type=190 (LJ14) 62 68 71: 168 type=192 (LJ14) 62 69 71: 169 type=194 (LJ14) 63 66 71: 170 type=186 (LJ14) 63 67 71: 171 type=194 (LJ14) 64 66 71: 172 type=186 (LJ14) 64 67 71: 173 type=196 (LJ14) 65 70 71: 174 type=197 (LJ14) 65 71 71: 175 type=198 (LJ14) 65 89 71: 176 type=190 (LJ14) 66 68 71: 177 type=195 (LJ14) 66 69 71: 178 type=186 (LJ14) 67 72 71: 179 type=186 (LJ14) 67 73 71: 180 type=187 (LJ14) 67 74 71: 181 type=188 (LJ14) 67 90 71: 182 type=189 (LJ14) 67 91 71: 183 type=190 (LJ14) 68 70 71: 184 type=190 (LJ14) 68 71 71: 185 type=190 (LJ14) 68 89 71: 186 type=191 (LJ14) 69 75 71: 187 type=191 (LJ14) 69 76 71: 188 type=192 (LJ14) 69 77 71: 189 type=190 (LJ14) 69 92 71: 190 type=192 (LJ14) 69 93 71: 191 type=193 (LJ14) 70 72 71: 192 type=193 (LJ14) 70 73 71: 193 type=191 (LJ14) 70 74 71: 194 type=194 (LJ14) 70 90 71: 195 type=186 (LJ14) 70 91 71: 196 type=191 (LJ14) 71 78 71: 197 type=191 (LJ14) 71 79 71: 198 type=187 (LJ14) 71 80 71: 199 type=195 (LJ14) 71 90 71: 200 type=187 (LJ14) 71 91 71: 201 type=193 (LJ14) 72 75 71: 202 type=193 (LJ14) 72 76 71: 203 type=191 (LJ14) 72 77 71: 204 type=196 (LJ14) 72 89 71: 205 type=193 (LJ14) 73 75 71: 206 type=193 (LJ14) 73 76 71: 207 type=191 (LJ14) 73 77 71: 208 type=196 (LJ14) 73 89 71: 209 type=190 (LJ14) 74 81 71: 210 type=207 (LJ14) 74 82 71: 211 type=197 (LJ14) 74 89 71: 212 type=193 (LJ14) 75 78 71: 213 type=193 (LJ14) 75 79 71: 214 type=186 (LJ14) 75 80 71: 215 type=193 (LJ14) 76 78 71: 216 type=193 (LJ14) 76 79 71: 217 type=186 (LJ14) 76 80 71: 218 type=187 (LJ14) 77 83 71: 219 type=187 (LJ14) 77 86 71: 220 type=190 (LJ14) 78 81 71: 221 type=208 (LJ14) 78 82 71: 222 type=190 (LJ14) 79 81 71: 223 type=208 (LJ14) 79 82 71: 224 type=190 (LJ14) 80 84 71: 225 type=190 (LJ14) 80 85 71: 226 type=190 (LJ14) 80 87 71: 227 type=190 (LJ14) 80 88 71: 228 type=190 (LJ14) 81 83 71: 229 type=190 (LJ14) 81 86 71: 230 type=190 (LJ14) 83 87 71: 231 type=190 (LJ14) 83 88 71: 232 type=190 (LJ14) 84 86 71: 233 type=190 (LJ14) 85 86 71: 234 type=196 (LJ14) 89 94 71: 235 type=197 (LJ14) 89 95 71: 236 type=198 (LJ14) 89 100 71: 237 type=190 (LJ14) 90 92 71: 238 type=195 (LJ14) 90 93 71: 239 type=186 (LJ14) 91 96 71: 240 type=186 (LJ14) 91 97 71: 241 type=209 (LJ14) 91 98 71: 242 type=188 (LJ14) 91 101 71: 243 type=189 (LJ14) 91 102 71: 244 type=190 (LJ14) 92 94 71: 245 type=190 (LJ14) 92 95 71: 246 type=190 (LJ14) 92 100 71: 247 type=190 (LJ14) 93 99 71: 248 type=190 (LJ14) 93 103 71: 249 type=192 (LJ14) 93 104 71: 250 type=193 (LJ14) 94 96 71: 251 type=193 (LJ14) 94 97 71: 252 type=210 (LJ14) 94 98 71: 253 type=194 (LJ14) 94 101 71: 254 type=186 (LJ14) 94 102 71: 255 type=195 (LJ14) 95 101 71: 256 type=187 (LJ14) 95 102 71: 257 type=190 (LJ14) 96 99 71: 258 type=196 (LJ14) 96 100 71: 259 type=190 (LJ14) 97 99 71: 260 type=196 (LJ14) 97 100 71: 261 type=211 (LJ14) 98 100 71: 262 type=196 (LJ14) 100 105 71: 263 type=197 (LJ14) 100 106 71: 264 type=198 (LJ14) 100 115 71: 265 type=190 (LJ14) 101 103 71: 266 type=195 (LJ14) 101 104 71: 267 type=186 (LJ14) 102 107 71: 268 type=186 (LJ14) 102 108 71: 269 type=187 (LJ14) 102 109 71: 270 type=188 (LJ14) 102 116 71: 271 type=189 (LJ14) 102 117 71: 272 type=190 (LJ14) 103 105 71: 273 type=190 (LJ14) 103 106 71: 274 type=190 (LJ14) 103 115 71: 275 type=191 (LJ14) 104 110 71: 276 type=191 (LJ14) 104 111 71: 277 type=197 (LJ14) 104 112 71: 278 type=190 (LJ14) 104 118 71: 279 type=192 (LJ14) 104 119 71: 280 type=193 (LJ14) 105 107 71: 281 type=193 (LJ14) 105 108 71: 282 type=191 (LJ14) 105 109 71: 283 type=194 (LJ14) 105 116 71: 284 type=186 (LJ14) 105 117 71: 285 type=195 (LJ14) 106 113 71: 286 type=195 (LJ14) 106 114 71: 287 type=195 (LJ14) 106 116 71: 288 type=187 (LJ14) 106 117 71: 289 type=193 (LJ14) 107 110 71: 290 type=193 (LJ14) 107 111 71: 291 type=196 (LJ14) 107 112 71: 292 type=196 (LJ14) 107 115 71: 293 type=193 (LJ14) 108 110 71: 294 type=193 (LJ14) 108 111 71: 295 type=196 (LJ14) 108 112 71: 296 type=196 (LJ14) 108 115 71: 297 type=197 (LJ14) 109 115 71: 298 type=194 (LJ14) 110 113 71: 299 type=194 (LJ14) 110 114 71: 300 type=194 (LJ14) 111 113 71: 301 type=194 (LJ14) 111 114 71: 302 type=196 (LJ14) 115 120 71: 303 type=197 (LJ14) 115 121 71: 304 type=198 (LJ14) 115 134 71: 305 type=190 (LJ14) 116 118 71: 306 type=195 (LJ14) 116 119 71: 307 type=186 (LJ14) 117 122 71: 308 type=186 (LJ14) 117 123 71: 309 type=187 (LJ14) 117 124 71: 310 type=188 (LJ14) 117 135 71: 311 type=189 (LJ14) 117 136 71: 312 type=190 (LJ14) 118 120 71: 313 type=190 (LJ14) 118 121 71: 314 type=190 (LJ14) 118 134 71: 315 type=191 (LJ14) 119 125 71: 316 type=192 (LJ14) 119 126 71: 317 type=192 (LJ14) 119 130 71: 318 type=190 (LJ14) 119 137 71: 319 type=192 (LJ14) 119 138 71: 320 type=193 (LJ14) 120 122 71: 321 type=193 (LJ14) 120 123 71: 322 type=191 (LJ14) 120 124 71: 323 type=194 (LJ14) 120 135 71: 324 type=186 (LJ14) 120 136 71: 325 type=191 (LJ14) 121 127 71: 326 type=191 (LJ14) 121 128 71: 327 type=191 (LJ14) 121 129 71: 328 type=191 (LJ14) 121 131 71: 329 type=191 (LJ14) 121 132 71: 330 type=191 (LJ14) 121 133 71: 331 type=195 (LJ14) 121 135 71: 332 type=187 (LJ14) 121 136 71: 333 type=193 (LJ14) 122 125 71: 334 type=191 (LJ14) 122 126 71: 335 type=191 (LJ14) 122 130 71: 336 type=196 (LJ14) 122 134 71: 337 type=193 (LJ14) 123 125 71: 338 type=191 (LJ14) 123 126 71: 339 type=191 (LJ14) 123 130 71: 340 type=196 (LJ14) 123 134 71: 341 type=197 (LJ14) 124 134 71: 342 type=193 (LJ14) 125 127 71: 343 type=193 (LJ14) 125 128 71: 344 type=193 (LJ14) 125 129 71: 345 type=193 (LJ14) 125 131 71: 346 type=193 (LJ14) 125 132 71: 347 type=193 (LJ14) 125 133 71: 348 type=191 (LJ14) 126 131 71: 349 type=191 (LJ14) 126 132 71: 350 type=191 (LJ14) 126 133 71: 351 type=191 (LJ14) 127 130 71: 352 type=191 (LJ14) 128 130 71: 353 type=191 (LJ14) 129 130 71: 354 type=196 (LJ14) 134 139 71: 355 type=197 (LJ14) 134 140 71: 356 type=198 (LJ14) 134 144 71: 357 type=190 (LJ14) 135 137 71: 358 type=195 (LJ14) 135 138 71: 359 type=186 (LJ14) 136 141 71: 360 type=186 (LJ14) 136 142 71: 361 type=186 (LJ14) 136 143 71: 362 type=188 (LJ14) 136 145 71: 363 type=189 (LJ14) 136 146 71: 364 type=190 (LJ14) 137 139 71: 365 type=190 (LJ14) 137 140 71: 366 type=190 (LJ14) 137 144 71: 367 type=190 (LJ14) 138 147 71: 368 type=192 (LJ14) 138 148 71: 369 type=193 (LJ14) 139 141 71: 370 type=193 (LJ14) 139 142 71: 371 type=193 (LJ14) 139 143 71: 372 type=194 (LJ14) 139 145 71: 373 type=186 (LJ14) 139 146 71: 374 type=195 (LJ14) 140 145 71: 375 type=187 (LJ14) 140 146 71: 376 type=196 (LJ14) 141 144 71: 377 type=196 (LJ14) 142 144 71: 378 type=196 (LJ14) 143 144 71: 379 type=196 (LJ14) 144 149 71: 380 type=197 (LJ14) 144 150 71: 381 type=198 (LJ14) 144 154 71: 382 type=190 (LJ14) 145 147 71: 383 type=195 (LJ14) 145 148 71: 384 type=186 (LJ14) 146 151 71: 385 type=186 (LJ14) 146 152 71: 386 type=186 (LJ14) 146 153 71: 387 type=188 (LJ14) 146 155 71: 388 type=190 (LJ14) 147 149 71: 389 type=190 (LJ14) 147 150 71: 390 type=190 (LJ14) 147 154 71: 391 type=193 (LJ14) 149 151 71: 392 type=193 (LJ14) 149 152 71: 393 type=193 (LJ14) 149 153 71: 394 type=194 (LJ14) 149 155 71: 395 type=195 (LJ14) 150 155 71: 396 type=196 (LJ14) 151 154 71: 397 type=196 (LJ14) 152 154 71: 398 type=196 (LJ14) 153 154 71: Coulomb-14: 71: nr: 0 71: LJC-14 q: 71: nr: 0 71: LJC Pairs NB: 71: nr: 0 71: LJ (SR): 71: nr: 0 71: Buck.ham (SR): 71: nr: 0 71: LJ: 71: nr: 0 71: B.ham: 71: nr: 0 71: Disper. corr.: 71: nr: 0 71: Coulomb (SR): 71: nr: 0 71: Coul: 71: nr: 0 71: RF excl.: 71: nr: 0 71: Coul. recip.: 71: nr: 0 71: LJ recip.: 71: nr: 0 71: DPD: 71: nr: 0 71: Polarization: 71: nr: 0 71: Water Pol.: 71: nr: 0 71: Thole Pol.: 71: nr: 0 71: Anharm. Pol.: 71: nr: 0 71: Position Rest.: 71: nr: 0 71: Flat-b. P-R.: 71: nr: 0 71: Dis. Rest.: 71: nr: 0 71: D.R.Viol. (nm): 71: nr: 0 71: Orient. Rest.: 71: nr: 0 71: Ori. R. RMSD: 71: nr: 0 71: Angle Rest.: 71: nr: 0 71: Angle Rest. Z: 71: nr: 0 71: Dih. Rest.: 71: nr: 0 71: Dih. Rest. Vi.: 71: nr: 0 71: Constraint: 71: nr: 0 71: Constr. No Co.: 71: nr: 0 71: Settle: 71: nr: 0 71: Virtual site 1: 71: nr: 0 71: Virtual site 2: 71: nr: 0 71: Virt. site 2fd: 71: nr: 0 71: Virtual site 3: 71: nr: 0 71: Virt. site 3fd: 71: nr: 0 71: Vir. site 3fad: 71: nr: 0 71: Vir. site 3out: 71: nr: 0 71: Virt. site 4fd: 71: nr: 0 71: Vir. site 4fdn: 71: nr: 0 71: Virtual site N: 71: nr: 0 71: COM Pull En.: 71: nr: 0 71: Dens. fitting: 71: nr: 0 71: Quantum En.: 71: nr: 0 71: NN Potential: 71: nr: 0 71: Potential: 71: nr: 0 71: Kinetic En.: 71: nr: 0 71: Total Energy: 71: nr: 0 71: Conserved En.: 71: nr: 0 71: Temperature: 71: nr: 0 71: Vir. Temp.: 71: nr: 0 71: Pres. DC: 71: nr: 0 71: Pressure: 71: nr: 0 71: dH/dl constr.: 71: nr: 0 71: dVremain/dl: 71: nr: 0 71: dEkin/dl: 71: nr: 0 71: dVcoul/dl: 71: nr: 0 71: dVvdw/dl: 71: nr: 0 71: dVbonded/dl: 71: nr: 0 71: dVrestraint/dl: 71: nr: 0 71: dVtemp/dl: 71: nr: 0 71: grp[T-Coupling ] nr=1, name=[ rest] 71: grp[Energy Mon. ] nr=1, name=[ rest] 71: grp[Acc. not used] nr=1, name=[ rest] 71: grp[Freeze ] nr=1, name=[ rest] 71: grp[User1 ] nr=1, name=[ rest] 71: grp[User2 ] nr=1, name=[ rest] 71: grp[VCM ] nr=1, name=[ rest] 71: grp[Compressed X] nr=1, name=[ rest] 71: grp[Or. Res. Fit] nr=1, name=[ rest] 71: grp[QMMM ] nr=1, name=[ rest] 71: grpname (11): 71: grpname[0]={name="System"} 71: grpname[1]={name="Protein"} 71: grpname[2]={name="Protein-H"} 71: grpname[3]={name="C-alpha"} 71: grpname[4]={name="Backbone"} 71: grpname[5]={name="MainChain"} 71: grpname[6]={name="MainChain+Cb"} 71: grpname[7]={name="MainChain+H"} 71: grpname[8]={name="SideChain"} 71: grpname[9]={name="SideChain-H"} 71: grpname[10]={name="rest"} 71: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 71: allocated 0 0 0 0 0 0 0 0 0 0 71: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 71: box (3x3): 71: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 71: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 71: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 71: box_rel (3x3): 71: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: boxv (3x3): 71: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: pres_prev (3x3): 71: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: svir_prev (3x3): 71: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: fvir_prev (3x3): 71: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: nosehoover_xi: not available 71: x (156x3): 71: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 71: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 71: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 71: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 71: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 71: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 71: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 71: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 71: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 71: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 71: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 71: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 71: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 71: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 71: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 71: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 71: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 71: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 71: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 71: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 71: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 71: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 71: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 71: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 71: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 71: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 71: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 71: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 71: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 71: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 71: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 71: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 71: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 71: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 71: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 71: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 71: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 71: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 71: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 71: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 71: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 71: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 71: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 71: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 71: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 71: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 71: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 71: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 71: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 71: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 71: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 71: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 71: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 71: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 71: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 71: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 71: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 71: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 71: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 71: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 71: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 71: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 71: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 71: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 71: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 71: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 71: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 71: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 71: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 71: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 71: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 71: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 71: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 71: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 71: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 71: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 71: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 71: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 71: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 71: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 71: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 71: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 71: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 71: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 71: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 71: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 71: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 71: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 71: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 71: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 71: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 71: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 71: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 71: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 71: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 71: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 71: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 71: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 71: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 71: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 71: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 71: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 71: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 71: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 71: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 71: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 71: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 71: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 71: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 71: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 71: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 71: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 71: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 71: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 71: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 71: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 71: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 71: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 71: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 71: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 71: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 71: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 71: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 71: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 71: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 71: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 71: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 71: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 71: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 71: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 71: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 71: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 71: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 71: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 71: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 71: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 71: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 71: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 71: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 71: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 71: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 71: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 71: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 71: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 71: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 71: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 71: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 71: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 71: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 71: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 71: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 71: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 71: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 71: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 71: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 71: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 71: v (156x3): 71: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: Group statistics 71: T-Coupling : 156 (total 156 atoms) 71: Energy Mon. : 156 (total 156 atoms) 71: Acc. not used: 156 (total 156 atoms) 71: Freeze : 156 (total 156 atoms) 71: User1 : 156 (total 156 atoms) 71: User2 : 156 (total 156 atoms) 71: VCM : 156 (total 156 atoms) 71: Compressed X: 156 (total 156 atoms) 71: Or. Res. Fit: 156 (total 156 atoms) 71: QMMM : 156 (total 156 atoms) 71: [ OK ] DumpTest.WorksWithTpr (13 ms) 71: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: [ OK ] DumpTest.WorksWithTprAndMdpWriting (2 ms) 71: [----------] 2 tests from DumpTest (15 ms total) 71: 71: [----------] 3 tests from HelpwritingTest 71: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 71: [ OK ] HelpwritingTest.ConvertTprWritesHelp (36 ms) 71: [ RUN ] HelpwritingTest.DumpWritesHelp 71: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 71: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 71: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 71: [----------] 3 tests from HelpwritingTest (38 ms total) 71: 71: [----------] 7 tests from GmxMakeNdx 71: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 71: 71: Reading structure file 71: Going to read 0 old index file(s) 71: Analysing residue names: 71: There are: 16 Protein residues 71: Analysing Protein... 71: 71: 0 System : 256 atoms 71: 1 Protein : 256 atoms 71: 2 Protein-H : 139 atoms 71: 3 C-alpha : 16 atoms 71: 4 Backbone : 48 atoms 71: 5 MainChain : 63 atoms 71: 6 MainChain+Cb : 78 atoms 71: 7 MainChain+H : 81 atoms 71: 8 SideChain : 175 atoms 71: 9 SideChain-H : 76 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (14 ms) 71: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 71: Going to read 1 old index file(s) 71: Deducing 22 atoms in the system from indices in the index file 71: 71: 0 System : 22 atoms 71: 1 Protein : 22 atoms 71: 2 Protein-H : 10 atoms 71: 3 C-alpha : 1 atoms 71: 4 Backbone : 5 atoms 71: 5 MainChain : 7 atoms 71: 6 MainChain+Cb : 8 atoms 71: 7 MainChain+H : 9 atoms 71: 8 SideChain : 13 atoms 71: 9 SideChain-H : 3 atoms 71: 10 CA : 1 atoms 71: 11 C_&_r_1 : 1 atoms 71: 12 C_&_r_2 : 1 atoms 71: 13 N_&_r_2 : 1 atoms 71: 14 N_&_r_3 : 1 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: Copied index group 1 'Protein' 71: Copied index group 2 'Protein-H' 71: Merged two groups with OR: 22 10 -> 22 71: 71: > 71: [ OK ] GmxMakeNdx.HandlesNoStructureInput (2 ms) 71: [ RUN ] GmxMakeNdx.HandlesNotProtein 71: Going to read 1 old index file(s) 71: Deducing 6 atoms in the system from indices in the index file 71: 71: 0 System : 6 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: [ OK ] GmxMakeNdx.HandlesNotProtein (8 ms) 71: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 71: Going to read 1 old index file(s) 71: Deducing 22 atoms in the system from indices in the index file 71: 71: 0 System : 22 atoms 71: 1 Protein : 22 atoms 71: 2 Protein-H : 10 atoms 71: 3 C-alpha : 1 atoms 71: 4 Backbone : 5 atoms 71: 5 MainChain : 7 atoms 71: 6 MainChain+Cb : 8 atoms 71: 7 MainChain+H : 9 atoms 71: 8 SideChain : 13 atoms 71: 9 SideChain-H : 3 atoms 71: 10 CA : 1 atoms 71: 11 C_&_r_1 : 1 atoms 71: 12 C_&_r_2 : 1 atoms 71: 13 N_&_r_2 : 1 atoms 71: 14 N_&_r_3 : 1 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: Copied index group 4 'Backbone' 71: Copied index group 8 'SideChain' 71: Merged two groups with AND: 5 13 -> 0 71: Group is empty 71: 71: > 71: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (1 ms) 71: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 71: Going to read 1 old index file(s) 71: Deducing 6 atoms in the system from indices in the index file 71: 71: 0 System : 6 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: Removed group 0 'System' 71: 71: > 71: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (1 ms) 71: [ RUN ] GmxMakeNdx.Splitres 71: 71: Reading structure file 71: Going to read 0 old index file(s) 71: Analysing residue names: 71: There are: 2 Water residues 71: 71: 0 System : 6 atoms 71: 1 Water : 6 atoms 71: 2 SOL : 6 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: Splitting group 1 'Water' into residues 71: 71: > 71: [ OK ] GmxMakeNdx.Splitres (2 ms) 71: [ RUN ] GmxMakeNdx.Splitat 71: 71: Reading structure file 71: Going to read 0 old index file(s) 71: Analysing residue names: 71: There are: 2 Water residues 71: 71: 0 System : 6 atoms 71: 1 Water : 6 atoms 71: 2 SOL : 6 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: Splitting group 1 'Water' into atoms 71: 71: > 71: [ OK ] GmxMakeNdx.Splitat (2 ms) 71: [----------] 7 tests from GmxMakeNdx (33 ms total) 71: 71: [----------] 4 tests from ReportMethodsTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Setting the LD random seed to -805994853 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 71: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 71: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 71: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 71: [ RUN ] ReportMethodsTest.WritesCorrectInformation 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: [ OK ] ReportMethodsTest.WritesCorrectInformation (1 ms) 71: [ RUN ] ReportMethodsTest.ToolEndToEndTest 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: section: Methods 71: subsection: Simulation system 71: A system of 1 molecules (156 atoms) was simulated. 71: 71: subsection: Simulation settings 71: A total of 0 ns were simulated with a time step of 1 fs. 71: Neighbor searching was performed every 10 steps. 71: The Cut-off algorithm was used for electrostatic interactions. 71: with a cut-off of 1 nm. 71: A single cut-off of 1.1 nm was used for Van der Waals interactions. 71: [ OK ] ReportMethodsTest.ToolEndToEndTest (1 ms) 71: [----------] 4 tests from ReportMethodsTest (2 ms total) 71: 71: [----------] 4 tests from ConvertTprTest 71: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Setting the LD random seed to -18351137 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: Input file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 0 71: Runtime for the run 0 ps 71: Run end step 0 71: Run end time 0 ps 71: 71: Extending remaining runtime by 100 ps 71: 71: Output file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 100000 71: Runtime for the run 100 ps 71: Run end step 100000 71: Run end time 100 ps 71: 71: Input file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 100000 71: Runtime for the run 100 ps 71: Run end step 100000 71: Run end time 100 ps 71: 71: Extending remaining runtime by 100 ps 71: 71: Output file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 200000 71: Runtime for the run 200 ps 71: Run end step 200000 71: Run end time 200 ps 71: 71: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (840 ms) 71: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Setting the LD random seed to -713162791 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: Input file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 0 71: Runtime for the run 0 ps 71: Run end step 0 71: Run end time 0 ps 71: 71: Extending remaining runtime to 100 ps 71: 71: Output file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 100000 71: Runtime for the run 100 ps 71: Run end step 100000 71: Run end time 100 ps 71: 71: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (845 ms) 71: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Setting nsteps to 102 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Setting the LD random seed to 1006628857 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: Input file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 0 71: Runtime for the run 0 ps 71: Run end step 0 71: Run end time 0 ps 71: 71: 71: Output file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 102 71: Runtime for the run 0.102 ps 71: Run end step 102 71: Run end time 0.102 ps 71: 71: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (836 ms) 71: [ RUN ] ConvertTprTest.generateVelocitiesTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Setting the LD random seed to -1075069045 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] ConvertTprTest.generateVelocitiesTest (882 ms) 71: [----------] 4 tests from ConvertTprTest (3405 ms total) 71: 71: [----------] 1 test from ConvertTprNoVelocityTest 71: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: 71: NOTE 3 [file lysozyme.top, line 1465]: 71: Zero-step energy minimization will alter the coordinates before 71: calculating the energy. If you just want the energy of a single point, 71: try zero-step MD (with unconstrained_start = yes). To do multiple 71: single-point energy evaluations of different configurations of the same 71: topology, use mdrun -rerun. 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 71: Setting the LD random seed to -2621846 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (852 ms) 71: [----------] 1 test from ConvertTprNoVelocityTest (852 ms total) 71: 71: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: trr version: GMX_trn_file (single precision) 71: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (2 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 71: ./src/gromacs/tools/tests/trjconv.cpp:86: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md (0 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 71: ./src/gromacs/tools/tests/trjconv.cpp:123: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md (0 ms) 71: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats (16 ms total) 71: 71: [----------] 35 tests from Works/TrjconvDumpTest 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 71: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 71: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 71: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 71: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 71: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 (0 ms) 71: [----------] 35 tests from Works/TrjconvDumpTest (30 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 70 tests from 8 test suites ran. (6083 ms total) 71: [ PASSED ] 63 tests. 71: [ SKIPPED ] 7 tests, listed below: 71: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 71: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 71/103 Test #71: ToolUnitTests ............................. Passed 6.12 sec test 72 Start 72: ToolWithLeaksUnitTests 72: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/ToolWithLeaksUnitTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests 72: Test timeout computed to be: 1920 72: [==========] Running 2 tests from 2 test suites. 72: [----------] Global test environment set-up. 72: [----------] 1 test from ConvertTprTest 72: [ RUN ] ConvertTprTest.selectIndexTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 72: Group 0 ( System) has 156 elements 72: Group 1 ( Protein) has 156 elements 72: Group 2 ( Protein-H) has 75 elements 72: Group 3 ( C-alpha) has 10 elements 72: Group 4 ( Backbone) has 30 elements 72: Group 5 ( MainChain) has 40 elements 72: Group 6 ( MainChain+Cb) has 49 elements 72: Group 7 ( MainChain+H) has 52 elements 72: Group 8 ( SideChain) has 104 elements 72: Group 9 ( SideChain-H) has 35 elements 72: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 72: Reduced ilist BONDS from 156 to 75 entries 72: Reduced ilist ANGLES from 281 to 98 entries 72: Reduced ilist PDIHS from 29 to 12 entries 72: Reduced ilist RBDIHS from 313 to 89 entries 72: Reduced ilist LJ14 from 399 to 107 entries 72: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 72: Setting the LD random seed to -1747085442 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Selected 2: 'Protein-H' 72: [ OK ] ConvertTprTest.selectIndexTest (865 ms) 72: [----------] 1 test from ConvertTprTest (865 ms total) 72: 72: [----------] 1 test from ConvertTprNoVelocityTest 72: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: 72: NOTE 3 [file lysozyme.top, line 1465]: 72: Zero-step energy minimization will alter the coordinates before 72: calculating the energy. If you just want the energy of a single point, 72: try zero-step MD (with unconstrained_start = yes). To do multiple 72: single-point energy evaluations of different configurations of the same 72: topology, use mdrun -rerun. 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 72: Group 0 ( System) has 156 elements 72: Group 1 ( Protein) has 156 elements 72: Group 2 ( Protein-H) has 75 elements 72: Group 3 ( C-alpha) has 10 elements 72: Group 4 ( Backbone) has 30 elements 72: Group 5 ( MainChain) has 40 elements 72: Group 6 ( MainChain+Cb) has 49 elements 72: Group 7 ( MainChain+H) has 52 elements 72: Group 8 ( SideChain) has 104 elements 72: Group 9 ( SideChain-H) has 35 elements 72: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 72: Reduced ilist BONDS from 156 to 75 entries 72: Reduced ilist ANGLES from 281 to 98 entries 72: Reduced ilist PDIHS from 29 to 12 entries 72: Reduced ilist RBDIHS from 313 to 89 entries 72: Reduced ilist LJ14 from 399 to 107 entries 72: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 72: Setting the LD random seed to -1896087555 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Selected 2: 'Protein-H' 72: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (835 ms) 72: [----------] 1 test from ConvertTprNoVelocityTest (835 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 2 tests from 2 test suites ran. (1701 ms total) 72: [ PASSED ] 2 tests. 72/103 Test #72: ToolWithLeaksUnitTests .................... Passed 1.73 sec test 73 Start 73: H5mdTests 73: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/h5md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/H5mdTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/h5md/tests 73: Test timeout computed to be: 30 73: [==========] Running 1 test from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 1 test from H5mdDisabledTest 73: [ RUN ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled 73: [ OK ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled (0 ms) 73: [----------] 1 test from H5mdDisabledTest (0 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (0 ms total) 73: [ PASSED ] 1 test. 73/103 Test #73: H5mdTests ................................. Passed 0.02 sec test 74 Start 74: FileIOTests 74: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/FileIOTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/fileio/tests 74: Test timeout computed to be: 30 74: [==========] Running 432 tests from 17 test suites. 74: [----------] Global test environment set-up. 74: [----------] 4 tests from Checkpoint 74: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 74: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 74: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 74: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 74: [ RUN ] Checkpoint.KvtRoundTripInt64 74: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 74: [ RUN ] Checkpoint.KvtRoundTripReal 74: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 74: [----------] 4 tests from Checkpoint (0 ms total) 74: 74: [----------] 1 test from StructureIOTest 74: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 74: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (1 ms) 74: [----------] 1 test from StructureIOTest (1 ms total) 74: 74: [----------] 2 tests from FileMD5Test 74: [ RUN ] FileMD5Test.CanComputeMD5 74: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 74: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 74: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 74: [----------] 2 tests from FileMD5Test (1 ms total) 74: 74: [----------] 4 tests from FileTypeTest 74: [ RUN ] FileTypeTest.CorrectValueForEmptyString 74: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 74: [ RUN ] FileTypeTest.CorrectValueForNoExtension 74: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 74: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 74: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 74: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 74: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 74: [----------] 4 tests from FileTypeTest (0 ms total) 74: 74: [----------] 4 tests from ColorMapTest 74: [ RUN ] ColorMapTest.CanReadFromFile 74: [ OK ] ColorMapTest.CanReadFromFile (1 ms) 74: [ RUN ] ColorMapTest.CanWriteToFile 74: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 74: [ RUN ] ColorMapTest.RoundTrip 74: [ OK ] ColorMapTest.RoundTrip (0 ms) 74: [ RUN ] ColorMapTest.SearchWorks 74: [ OK ] ColorMapTest.SearchWorks (0 ms) 74: [----------] 4 tests from ColorMapTest (2 ms total) 74: 74: [----------] 4 tests from MatioTest 74: [ RUN ] MatioTest.CanWriteToFile 74: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 74: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 74: Converted a 4x3 matrix with 4 levels to reals 74: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 74: [ RUN ] MatioTest.CanConvertToNewRealMatrix 74: Converted a 4x3 matrix with 4 levels to reals 74: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 74: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 74: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (3 ms) 74: [----------] 4 tests from MatioTest (4 ms total) 74: 74: [----------] 3 tests from MrcSerializer 74: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 74: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 74: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 74: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 74: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 74: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 74: [----------] 3 tests from MrcSerializer (0 ms total) 74: 74: [----------] 4 tests from MrcDensityMap 74: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 74: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 74: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 74: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 74: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 74: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 74: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 74: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms) 74: [----------] 4 tests from MrcDensityMap (3 ms total) 74: 74: [----------] 8 tests from MrcDensityMapHeaderTest 74: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 74: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 74: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 74: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 74: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 74: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 74: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 74: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.IsSane 74: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 74: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 74: 74: [----------] 10 tests from ReadTest 74: [ RUN ] ReadTest.get_eint_ReadsInteger 74: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 74: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 74: 74: ERROR 1 [file unknown]: 74: Right hand side '0.8' for parameter 'test' in parameter file is not an 74: integer value 74: 74: 74: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 74: [ RUN ] ReadTest.get_eint_WarnsAboutString 74: 74: ERROR 1 [file unknown]: 74: Right hand side 'hello' for parameter 'test' in parameter file is not an 74: integer value 74: 74: 74: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 74: [ RUN ] ReadTest.get_eint64_ReadsInteger 74: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 74: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 74: 74: ERROR 1 [file unknown]: 74: Right hand side '0.8' for parameter 'test' in parameter file is not an 74: integer value 74: 74: 74: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 74: [ RUN ] ReadTest.get_eint64_WarnsAboutString 74: 74: ERROR 1 [file unknown]: 74: Right hand side 'hello' for parameter 'test' in parameter file is not an 74: integer value 74: 74: 74: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 74: [ RUN ] ReadTest.get_ereal_ReadsInteger 74: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 74: [ RUN ] ReadTest.get_ereal_ReadsFloat 74: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 74: [ RUN ] ReadTest.get_ereal_WarnsAboutString 74: 74: ERROR 1 [file unknown]: 74: Right hand side 'hello' for parameter 'test' in parameter file is not a 74: real value 74: 74: 74: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 74: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 74: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 74: [----------] 10 tests from ReadTest (0 ms total) 74: 74: [----------] 3 tests from TimeControlTest 74: [ RUN ] TimeControlTest.UnSetHasNoValue 74: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 74: [ RUN ] TimeControlTest.CanSetValue 74: [ OK ] TimeControlTest.CanSetValue (0 ms) 74: [ RUN ] TimeControlTest.CanUnsetValueAgain 74: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 74: [----------] 3 tests from TimeControlTest (0 ms total) 74: 74: [----------] 1 test from TngTest 74: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 74: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 74: [----------] 1 test from TngTest (0 ms total) 74: 74: [----------] 4 tests from XvgioTest 74: [ RUN ] XvgioTest.readXvgIntWorks 74: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 74: [ RUN ] XvgioTest.readXvgRealWorks 74: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 74: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 74: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 74: [ RUN ] XvgioTest.readXvgDeprecatedWorks 74: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 74: [----------] 4 tests from XvgioTest (0 ms total) 74: 74: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 74: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 74: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms) 74: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 74: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 74: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 74: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 74: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 74: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 74: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (3 ms total) 74: 74: [----------] 370 tests from FileTypeMatch/FileTypeTest 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (1 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 (0 ms) 74: [----------] 370 tests from FileTypeMatch/FileTypeTest (6 ms total) 74: 74: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest 74: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 74: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 (0 ms) 74: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 74: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 (0 ms) 74: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest (0 ms total) 74: 74: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 74: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 74: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (1 ms) 74: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 74: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 74: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 74: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 74: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 74: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 74: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (2 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 432 tests from 17 test suites ran. (30 ms total) 74: [ PASSED ] 432 tests. 74/103 Test #74: FileIOTests ............................... Passed 0.08 sec test 75 Start 75: SelectionUnitTests 75: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/SelectionUnitTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/gromacs/selection/tests 75: Test timeout computed to be: 30 75: [==========] Running 202 tests from 11 test suites. 75: [----------] Global test environment set-up. 75: [----------] 1 test from IndexGroupTest 75: [ RUN ] IndexGroupTest.RemovesDuplicates 75: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 75: [----------] 1 test from IndexGroupTest (0 ms total) 75: 75: [----------] 15 tests from IndexBlockTest 75: [ RUN ] IndexBlockTest.CreatesUnknownBlock 75: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 75: [ RUN ] IndexBlockTest.CreatesAtomBlock 75: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 75: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 75: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 75: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 75: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 75: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 75: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 75: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 75: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 75: [ RUN ] IndexBlockTest.CreatesSingleBlock 75: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 75: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 75: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 75: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 75: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 75: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 75: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 75: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 75: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 75: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 75: [----------] 15 tests from IndexBlockTest (4 ms total) 75: 75: [----------] 11 tests from IndexMapTest 75: [ RUN ] IndexMapTest.InitializesAtomBlock 75: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 75: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 75: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 75: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 75: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 75: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 75: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 75: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 75: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 75: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 75: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 75: [ RUN ] IndexMapTest.InitializesMoleculeBlock 75: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 75: [ RUN ] IndexMapTest.MapsSingleBlock 75: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 75: [ RUN ] IndexMapTest.MapsResidueBlocks 75: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 75: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 75: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 75: [ RUN ] IndexMapTest.HandlesMultipleRequests 75: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 75: [----------] 11 tests from IndexMapTest (6 ms total) 75: 75: [----------] 3 tests from IndexGroupsAndNamesTest 75: [ RUN ] IndexGroupsAndNamesTest.containsNames 75: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 75: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 75: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 75: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 75: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 75: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 75: 75: [----------] 15 tests from NeighborhoodSearchTest 75: [ RUN ] NeighborhoodSearchTest.SimpleSearch 75: [ OK ] NeighborhoodSearchTest.SimpleSearch (30 ms) 75: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 75: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (29 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearchBox 75: [ OK ] NeighborhoodSearchTest.GridSearchBox (4 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 75: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (11 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 75: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (6 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 75: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (2 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 75: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (3 ms) 75: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 75: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 75: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (60 ms) 75: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 75: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 75: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 75: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 75: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 75: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 75: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 75: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 75: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 75: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (7 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 75: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 75: [----------] 15 tests from NeighborhoodSearchTest (159 ms total) 75: 75: [----------] 13 tests from PositionCalculationTest 75: [ RUN ] PositionCalculationTest.ComputesAtomPositions 75: [ OK ] PositionCalculationTest.ComputesAtomPositions (36 ms) 75: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 75: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 75: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 75: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 75: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 75: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 75: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 75: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesPositionMask 75: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 75: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 75: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 75: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 75: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 75: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 75: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 75: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 75: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 75: [----------] 13 tests from PositionCalculationTest (43 ms total) 75: 75: [----------] 33 tests from SelectionCollectionTest 75: [ RUN ] SelectionCollectionTest.HandlesNoSelections 75: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 75: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms) 75: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 75: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 75: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 75: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 75: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 75: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 75: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms) 75: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 75: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 75: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 75: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 75: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 75: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 75: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 75: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 75: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 75: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 75: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 75: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 75: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 75: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 75: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 75: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 75: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 75: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 75: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 75: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 75: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 75: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 75: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 75: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 75: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 75: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 75: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 75: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 75: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 75: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 75: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (1 ms) 75: [----------] 33 tests from SelectionCollectionTest (26 ms total) 75: 75: [----------] 14 tests from SelectionCollectionInteractiveTest 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 75: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 75: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 75: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 75: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 75: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 75: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 75: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 75: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 75: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 75: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 75: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 75: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 75: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 75: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 75: [----------] 14 tests from SelectionCollectionInteractiveTest (14 ms total) 75: 75: [----------] 71 tests from SelectionCollectionDataTest 75: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 75: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 75: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesResnr 75: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 75: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 75: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 75: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 75: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 75: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesChain 75: [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesMass 75: [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesCharge 75: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 75: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 75: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 75: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesBeta 75: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesResname 75: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 75: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 75: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 75: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 75: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (2 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 75: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 75: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 75: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 75: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (4 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 75: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (3 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 75: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (3 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 75: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (3 ms) 75: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 75: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (2 ms) 75: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 75: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 75: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 75: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 75: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 75: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 75: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (2 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 75: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 75: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 75: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 75: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 75: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 75: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 75: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 75: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 75: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 75: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 75: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 75: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 75: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 75: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 75: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 75: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 75: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsVariableInArithmetic 75: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsVariableInArithmetic (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 75: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (2 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 75: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (2 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 75: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 75: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 75: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 75: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 75: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 75: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 75: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 75: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 75: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 75: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 75: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 75: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 75: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 75: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 75: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (3 ms) 75: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 75: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (3 ms) 75: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 75: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (2 ms) 75: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 75: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (3 ms) 75: [----------] 71 tests from SelectionCollectionDataTest (121 ms total) 75: 75: [----------] 17 tests from SelectionOptionTest 75: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 75: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 75: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 75: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 75: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 75: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 75: [ RUN ] SelectionOptionTest.ChecksEmptySelections 75: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 75: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 75: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesTooManySelections 75: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 75: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 75: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesAdjuster 75: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 75: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 75: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 75: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 75: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 75: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 75: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 75: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 75: [----------] 17 tests from SelectionOptionTest (10 ms total) 75: 75: [----------] 9 tests from SelectionFileOptionTest 75: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 75: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 75: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 75: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 75: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 75: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 75: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 75: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 75: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 75: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 75: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 75: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 75: [----------] 9 tests from SelectionFileOptionTest (6 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 202 tests from 11 test suites ran. (394 ms total) 75: [ PASSED ] 202 tests. 75/103 Test #75: SelectionUnitTests ........................ Passed 0.43 sec test 76 Start 76: MdrunOutputTests 76: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunOutputTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 12 tests from 5 test suites. 76: [----------] Global test environment set-up. 76: [----------] 1 test from MdrunTest 76: [ RUN ] MdrunTest.WritesHelp 76: [ OK ] MdrunTest.WritesHelp (20 ms) 76: [----------] 1 test from MdrunTest (20 ms total) 76: 76: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 76: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 2573.591 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 1 steps, 0.0 ps. 76: Setting the LD random seed to -302254610 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.057 0.029 199.4 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 6.039 3.974 14.307 0.000 76: Reading frame 0 time 0.000 76: # Atoms 6 76: Reading frame 1 time 0.001 Last frame 1 time 0.001 76: 76: 76: Item #frames Timestep (ps) 76: Step 2 0.001 76: Time 2 0.001 76: Lambda 0 76: Coords 2 0.001 76: Velocities 0 76: Forces 0 76: Box 2 0.001 76: Checking file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 76: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (43 ms) 76: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 2573.591 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 1 steps, 0.0 ps. 76: Setting the LD random seed to -2053 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.021 0.011 198.5 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 16.345 1.468 5.286 0.001 76: Reading frame 0 time 0.000 76: # Atoms 6 76: Reading frame 1 time 0.001 Last frame 1 time 0.001 76: 76: 76: Item #frames Timestep (ps) 76: Step 2 0.001 76: Time 2 0.001 76: Lambda 0 76: Coords 2 0.001 76: Velocities 0 76: Forces 0 76: Box 2 0.001 76: Checking file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 76: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (23 ms) 76: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 76: NVE simulation: will use the initial temperature of 2573.591 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 1 steps, 0.0 ps. 76: Setting the LD random seed to -546112184 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.022 0.011 198.6 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 15.597 1.539 5.540 0.001 76: Reading frame 0 time 0.000 76: # Atoms 3 76: Reading frame 1 time 0.001 Last frame 1 time 0.001 76: 76: 76: Item #frames Timestep (ps) 76: Step 2 0.001 76: Time 2 0.001 76: Lambda 0 76: Coords 2 0.001 76: Velocities 0 76: Forces 0 76: Box 2 0.001 76: Checking file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 76: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (23 ms) 76: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (91 ms total) 76: 76: [----------] 2 tests from Argon12/OutputFiles 76: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Number of degrees of freedom in T-Coupling group System is 33.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 68.810 K for 76: determining the Verlet buffer size 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Argon' 76: 16 steps, 0.0 ps. 76: Generated 1 of the 1 non-bonded parameter combinations 76: 76: Excluding 1 bonded neighbours molecule type 'Argon' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.031 0.016 199.0 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 93.328 0.257 0.926 0.013 76: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (28 ms) 76: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Number of degrees of freedom in T-Coupling group System is 33.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 68.810 K for 76: determining the Verlet buffer size 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Argon' 76: 16 steps, 0.0 ps. 76: Generated 1 of the 1 non-bonded parameter combinations 76: 76: Excluding 1 bonded neighbours molecule type 'Argon' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.028 0.014 199.4 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 103.510 0.232 0.835 0.014 76: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (30 ms) 76: [----------] 2 tests from Argon12/OutputFiles (59 ms total) 76: 76: [----------] 3 tests from MdrunCanWrite/Trajectories 76: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 6 steps, 0.0 ps. 76: Setting the LD random seed to -1342177441 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.028 0.014 198.6 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 43.043 0.558 2.007 0.003 76: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (31 ms) 76: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 6 steps, 0.0 ps. 76: Setting the LD random seed to -144745354 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.029 0.014 198.7 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 41.895 0.573 2.062 0.003 76: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (29 ms) 76: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 6 steps, 0.0 ps. 76: Setting the LD random seed to -272912899 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.019 0.010 198.1 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 63.099 0.380 1.369 0.004 76: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (24 ms) 76: [----------] 3 tests from MdrunCanWrite/Trajectories (86 ms total) 76: 76: [----------] 3 tests from MdrunCanWrite/NptTrajectories 76: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 2 steps, 0.0 ps. 76: Setting the LD random seed to -18893713 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.018 0.009 198.2 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 27.862 0.861 3.101 0.002 76: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (24 ms) 76: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 76: The Berendsen barostat does not generate any strictly correct ensemble, 76: and should not be used for new production simulations (in our opinion). 76: We recommend using the C-rescale barostat instead. 76: 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: 76: There was 1 WARNING 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 2 steps, 0.0 ps. 76: Setting the LD random seed to -1449183489 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.019 0.010 198.2 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 26.824 0.895 3.221 0.002 76: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (25 ms) 76: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 2 steps, 0.0 ps. 76: Setting the LD random seed to -2129986 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.018 0.009 198.1 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 29.017 0.827 2.978 0.002 76: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (23 ms) 76: [----------] 3 tests from MdrunCanWrite/NptTrajectories (73 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 12 tests from 5 test suites ran. (391 ms total) 76: [ PASSED ] 12 tests. 76/103 Test #76: MdrunOutputTests .......................... Passed 0.42 sec test 77 Start 77: MdrunModulesTests 77: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunModulesTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 15 tests from 3 test suites. 77: [----------] Global test environment set-up. 77: [----------] 9 tests from DensityFittingTest 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 2 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 3 steps. 77: Potential Energy = -3.8565254e+03 77: Maximum force = 4.5099883e+03 on atom 3 77: Norm of force = 1.6816849e+03 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1180673 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (16 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 2 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 3 steps. 77: Potential Energy = -9.8207725e+03 77: Maximum force = 7.3954834e+03 on atom 2 77: Norm of force = 2.7825089e+03 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1208094977 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (15 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 77: 77: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (12 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Overriding nsteps with value passed on the command line: 4 steps 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 4 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 5 steps. 77: Potential Energy = -5.4739321e+03 77: Maximum force = 6.1322017e+03 on atom 2 77: Norm of force = 1.7702150e+03 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -36831316 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (15 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 77: 77: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (11 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 2 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 3 steps. 77: Potential Energy = -3.8565254e+03 77: Maximum force = 4.5099883e+03 on atom 3 77: Norm of force = 1.6816849e+03 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -2621442 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (13 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 2 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 3 steps. 77: Potential Energy = -2.7138664e+04 77: Maximum force = 6.7827656e+03 on atom 2 77: Norm of force = 1.9608866e+03 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1677745157 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (14 ms) 77: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 77: 77: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 77: Setting the LD random seed to -1075217417 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 77: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (13 ms) 77: [ RUN ] DensityFittingTest.CheckpointWorks 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (2) 77: 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to 1038614301 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.037 0.019 199.2 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 13.935 1.722 6.200 0.002 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 77: Can not increase nstlist because an NVE ensemble is used 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.017 0.008 198.3 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 51.100 0.470 1.691 0.007 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (44 ms) 77: [----------] 9 tests from DensityFittingTest (156 ms total) 77: 77: [----------] 4 tests from MimicTest 77: [ RUN ] MimicTest.OneQuantumMol 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 21.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 77: NVE simulation with an initial temperature of zero: will use a Verlet 77: buffer of 10%. Check your energy drift! 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 77: 77: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 77: Reading frame 0 time 0.000 Last frame 0 time 0.000 77: 77: NOTE: 17 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.000 184.2 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 227.345 0.106 0.380 0.032 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1072945151 77: 77: Generated 10 of the 10 non-bonded parameter combinations 77: 77: Generated 10 of the 10 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] MimicTest.OneQuantumMol (15 ms) 77: [ RUN ] MimicTest.AllQuantumMol 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 21.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 77: NVE simulation with an initial temperature of zero: will use a Verlet 77: buffer of 10%. Check your energy drift! 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 77: 77: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 77: Reading frame 0 time 0.000 Last frame 0 time 0.000 77: 77: NOTE: 15 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.000 184.1 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 266.854 0.090 0.324 0.037 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -9326691 77: 77: Generated 10 of the 10 non-bonded parameter combinations 77: 77: Generated 10 of the 10 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] MimicTest.AllQuantumMol (15 ms) 77: [ RUN ] MimicTest.TwoQuantumMol 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 21.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 77: NVE simulation with an initial temperature of zero: will use a Verlet 77: buffer of 10%. Check your energy drift! 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 77: 77: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 77: Reading frame 0 time 0.000 Last frame 0 time 0.000 77: 77: NOTE: 14 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.000 185.1 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 267.445 0.090 0.323 0.037 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 752187130 77: 77: Generated 10 of the 10 non-bonded parameter combinations 77: 77: Generated 10 of the 10 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] MimicTest.TwoQuantumMol (13 ms) 77: [ RUN ] MimicTest.BondCuts 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 66.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 77: NVE simulation: will use the initial temperature of 300.368 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 77: 77: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 77: Reading frame 0 time 0.000 Last frame 0 time 0.000 77: 77: NOTE: 13 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 189.6 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 153.750 0.156 0.562 0.041 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -26214411 77: 77: Generated 2211 of the 2211 non-bonded parameter combinations 77: 77: Generated 2211 of the 2211 1-4 parameter combinations 77: 77: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] MimicTest.BondCuts (30 ms) 77: [----------] 4 tests from MimicTest (75 ms total) 77: 77: [----------] 2 tests from WithIntegrator/ImdTest 77: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 77: Generating 1-4 interactions: fudge = 1 77: 77: NOTE 1 [file glycine_vacuo.top, line 12]: 77: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 77: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 77: the time step of 2.0e-03 ps. 77: Maybe you forgot to change the constraints mdp option. 77: 77: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: IMD: Enabled. This simulation will accept incoming IMD connections. 77: IMD: Pulling from IMD remote is enabled (-imdpull). 77: IMD: Setting port for connection requests to 0. 77: IMD: Setting up incoming socket. 77: IMD: Listening for IMD connection on port 58255. 77: IMD: -imdwait not set, starting simulation. 77: starting mdrun 'Glycine' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to 1073737567 77: 77: Generated 20503 of the 20503 non-bonded parameter combinations 77: 77: Generated 17396 of the 20503 1-4 parameter combinations 77: 77: Excluding 3 bonded neighbours molecule type 'Glycine' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 14 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.069 0.035 199.4 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 14.926 1.608 11.577 0.001 77: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (244 ms) 77: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 77: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 77: apply to steep. 77: 77: Generating 1-4 interactions: fudge = 1 77: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: IMD: Enabled. This simulation will accept incoming IMD connections. 77: IMD: Pulling from IMD remote is enabled (-imdpull). 77: IMD: Setting port for connection requests to 0. 77: IMD: Setting up incoming socket. 77: IMD: Listening for IMD connection on port 55051. 77: IMD: -imdwait not set, starting simulation. 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 2 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 3 steps. 77: Potential Energy = 1.1977065e+03 77: Maximum force = 1.7794877e+04 on atom 9 77: Norm of force = 7.8732901e+03 77: Setting the LD random seed to -142740513 77: 77: Generated 20503 of the 20503 non-bonded parameter combinations 77: 77: Generated 17396 of the 20503 1-4 parameter combinations 77: 77: Excluding 3 bonded neighbours molecule type 'Glycine' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (195 ms) 77: [----------] 2 tests from WithIntegrator/ImdTest (439 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 15 tests from 3 test suites ran. (718 ms total) 77: [ PASSED ] 15 tests. 77/103 Test #77: MdrunModulesTests ......................... Passed 0.75 sec test 78 Start 78: MdrunIOTests 78: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunIOTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 76 tests from 13 test suites. 78: [----------] Global test environment set-up. 78: [----------] 9 tests from GromppTest 78: [ RUN ] GromppTest.EmptyMdpFileWorks 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -25038091 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.EmptyMdpFileWorks (10 ms) 78: [ RUN ] GromppTest.SimulatedAnnealingWorks 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Simulated annealing for group rest: Periodic, 4 timepoints 78: Time (ps) Temperature (K) 78: 0.0 298.0 78: 2.0 320.0 78: 4.0 320.0 78: 6.0 298.0 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -2622473 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.SimulatedAnnealingWorks (8 ms) 78: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Simulated annealing for group Methanol: Single, 3 timepoints 78: Time (ps) Temperature (K) 78: 0.0 298.0 78: 3.0 280.0 78: 6.0- 270.0 78: Simulated annealing for group SOL: Periodic, 4 timepoints 78: Time (ps) Temperature (K) 78: 0.0 298.0 78: 2.0 320.0 78: 4.0 320.0 78: 6.0 298.0 78: Number of degrees of freedom in T-Coupling group Methanol is 7.20 78: Number of degrees of freedom in T-Coupling group SOL is 4.80 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -33832194 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (9 ms) 78: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 78: Setting the LD random seed to 2134830781 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (13 ms) 78: [ RUN ] GromppTest.HandlesMaxwarn 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Number of degrees of freedom in T-Coupling group System is 12.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: Setting the LD random seed to -1350778945 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.HandlesMaxwarn (8 ms) 78: [ RUN ] GromppTest.MaxwarnShouldBePositive 78: [ OK ] GromppTest.MaxwarnShouldBePositive (1 ms) 78: [ RUN ] GromppTest.ValidTransformationCoord 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Pull group 1 'SOL' has 3 atoms 78: Pull group 2 'Methanol' has 3 atoms 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 5 78: 2 3 2 0.613 nm 0.000 nm 78: 0.613 nm 0.000 nm 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -402825217 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.ValidTransformationCoord (10 ms) 78: [ RUN ] GromppTest.InvalidTransformationCoord 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Pull group 1 'SOL' has 3 atoms 78: Pull group 2 'Methanol' has 3 atoms 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 5 78: 2 3 2 0.613 nm 0.000 nm 78: Setting the LD random seed to -411304513 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: [ OK ] GromppTest.InvalidTransformationCoord (10 ms) 78: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 78: Setting the LD random seed to 2112868346 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (12 ms) 78: [----------] 9 tests from GromppTest (84 ms total) 78: 78: [----------] 6 tests from MdrunTerminationTest 78: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -270807842 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.113 0.056 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 4.597 5.221 18.794 0.000 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Setting nsteps to 4 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 2 78: Runtime for the run 0.002 ps 78: Run end step 2 78: Run end time 0.002 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.012 0.006 197.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 41.373 0.580 2.088 0.003 78: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (82 ms) 78: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 1, rlist from 1.032 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 100 steps, 0.1 ps. 78: 78: Step 4: Run time exceeded 0.000 hours, will terminate the run within 200 steps 78: Setting the LD random seed to -17416477 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: NOTE: 12 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 667.004 0.036 0.130 0.046 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Setting nsteps to 102 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 100 78: Runtime for the run 0.1 ps 78: Run end step 100 78: Run end time 0.1 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 102 78: Runtime for the run 0.102 ps 78: Run end step 102 78: Run end time 0.102 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.010 0.005 197.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.336 0.486 1.751 0.003 78: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (36 ms) 78: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -95977985 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.016 0.008 198.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 31.988 0.750 2.701 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Setting nsteps to 4 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 2 78: Runtime for the run 0.002 ps 78: Run end step 2 78: Run end time 0.002 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.019 0.009 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 27.446 0.874 3.148 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Setting nsteps to 6 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 6 78: Runtime for the run 0.006 ps 78: Run end step 6 78: Run end time 0.006 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.019 0.010 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 26.741 0.897 3.231 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Setting nsteps to 8 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 6 78: Runtime for the run 0.006 ps 78: Run end step 6 78: Run end time 0.006 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 8 78: Runtime for the run 0.008 ps 78: Run end step 8 78: Run end time 0.008 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.012 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 22.347 1.074 3.866 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: NOTE: 22 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.000 0.000 169.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 415.582 0.058 0.208 0.029 78: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (76 ms) 78: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -35135570 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.021 0.011 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 24.524 0.979 3.523 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Setting nsteps to 4 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 4 steps, 0.0 ps. 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 2 78: Runtime for the run 0.002 ps 78: Run end step 2 78: Run end time 0.002 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.019 0.010 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 44.851 0.535 1.926 0.003 78: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (39 ms) 78: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -1082524165 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.013 0.007 197.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 38.560 0.622 2.241 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Setting nsteps to 4 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 2 78: Runtime for the run 0.002 ps 78: Run end step 2 78: Run end time 0.002 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (21 ms) 78: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -38969369 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.022 0.011 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 23.787 1.009 3.632 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Setting nsteps to 4 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 2 78: Runtime for the run 0.002 ps 78: Run end step 2 78: Run end time 0.002 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.021 0.010 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 25.165 0.954 3.433 0.002 78: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (40 ms) 78: [----------] 6 tests from MdrunTerminationTest (296 ms total) 78: 78: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 78: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.015 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 95.587 0.251 0.904 0.007 78: trr version: GMX_trn_file (single precision) 78: 78: 78: Will write trr: Trajectory in portable xdr format 78: Last frame -1 time 0.016 78: -> frame 0 time 0.016 78: Last written: frame 0 time 0.016 78: 78: 78: Will write trr: Trajectory in portable xdr format 78: Last frame -1 time 0.016 78: 78: Dumping frame at t= 0.016 ps 78: -> frame 0 time 0.016 78: Last written: frame 0 time 0.016 78: 78: 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Last frame -1 time 0.016 78: 78: There were 3 NOTEs 78: Note that major changes are planned in future for trjconv, to improve usability and utility. 78: Note that major changes are planned in future for trjconv, to improve usability and utility. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: Analysing residue names: 78: There are: 2 Water residues 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: Reading Coordinates, Velocities and Box size from old trajectory 78: 78: Will read whole trajectory 78: 78: Using frame at t = 0.016 ps 78: 78: Starting time for run is 0 ps 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (41 ms) 78: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.025 0.013 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 115.091 0.209 0.751 0.008 78: 78: 78: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (25 ms) 78: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (67 ms total) 78: 78: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.013 0.007 197.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 216.770 0.111 0.399 0.030 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.013 0.006 197.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 121.065 0.198 0.714 0.017 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.020 0.010 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 78.017 0.308 1.107 0.011 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (53 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.012 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 127.057 0.189 0.680 0.018 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.033 0.016 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 47.311 0.507 1.826 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.025 0.013 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 61.151 0.392 1.413 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (69 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.015 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 95.968 0.250 0.900 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.030 0.015 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 50.940 0.471 1.696 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.028 0.014 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 55.436 0.433 1.559 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (74 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.013 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 109.801 0.219 0.787 0.015 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 58.700 0.409 1.472 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.019 0.010 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 81.295 0.295 1.063 0.011 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (65 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.019 0.010 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 150.862 0.159 0.573 0.021 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.035 0.017 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 44.625 0.538 1.936 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.022 0.011 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 71.366 0.336 1.211 0.010 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (67 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.015 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 95.451 0.251 0.905 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.025 0.013 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 62.040 0.387 1.393 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.011 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 68.102 0.352 1.269 0.009 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (70 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.028 0.014 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 104.075 0.231 0.830 0.014 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.024 0.012 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 64.881 0.370 1.332 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.018 0.009 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 84.257 0.285 1.025 0.012 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (65 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.073 0.037 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 39.909 0.601 2.165 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.024 0.012 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 64.505 0.372 1.339 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.024 0.012 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 64.681 0.371 1.336 0.009 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (91 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.015 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 100.823 0.238 0.857 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.033 0.016 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 47.204 0.508 1.830 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.030 0.015 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 50.933 0.471 1.696 0.004 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (79 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.014 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 101.809 0.236 0.849 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.014 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 54.079 0.444 1.598 0.004 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.576 0.788 200.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 0.987 24.323 87.563 0.000 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (852 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.036 0.018 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 80.677 0.297 1.071 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.030 0.015 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 51.504 0.466 1.678 0.004 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.037 0.018 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 42.381 0.566 2.039 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (82 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.021 0.011 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 139.633 0.172 0.619 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.025 0.012 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 62.469 0.384 1.383 0.004 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.013 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 57.974 0.414 1.490 0.004 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (66 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.015 0.007 198.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 196.335 0.122 0.440 0.014 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.058 0.029 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 26.653 0.900 3.242 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 48.418 0.496 1.784 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (84 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.036 0.018 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 81.768 0.294 1.057 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.304 0.530 1.907 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 48.199 0.498 1.793 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (88 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 85.366 0.281 1.012 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.015 0.007 198.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 105.053 0.228 0.822 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.016 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.779 0.482 1.736 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (71 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.025 0.012 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 118.348 0.203 0.730 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.024 0.012 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 64.110 0.374 1.348 0.004 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.015 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 50.350 0.477 1.716 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (71 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.038 0.019 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 76.828 0.312 1.125 0.026 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.017 0.008 197.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 93.037 0.258 0.929 0.031 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.020 0.010 198.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 75.210 0.319 1.149 0.025 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (109 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.015 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 99.289 0.242 0.870 0.033 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.022 0.011 198.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 69.647 0.345 1.241 0.023 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.022 0.011 198.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 68.844 0.349 1.255 0.023 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (107 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.039 0.020 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 75.161 0.319 1.150 0.025 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.016 0.008 197.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 98.944 0.243 0.873 0.033 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.016 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.981 0.480 1.729 0.017 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (113 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.033 0.016 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 89.228 0.269 0.968 0.030 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.025 0.013 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 60.911 0.394 1.418 0.020 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.016 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.878 0.481 1.732 0.017 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (115 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.039 0.020 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 75.184 0.319 1.149 0.025 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.631 0.526 1.893 0.015 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 48.934 0.490 1.766 0.016 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (176 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.050 0.025 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 59.092 0.406 1.462 0.020 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.037 0.019 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 41.395 0.580 2.087 0.014 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.014 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 53.746 0.447 1.608 0.018 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (357 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.016 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 93.793 0.256 0.921 0.031 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 59.092 0.406 1.462 0.020 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 58.453 0.411 1.478 0.020 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (154 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.030 0.015 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 96.214 0.249 0.898 0.032 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 58.803 0.408 1.469 0.020 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.014 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 56.532 0.425 1.528 0.019 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (199 ms) 78: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (3288 ms total) 78: 78: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.042 0.021 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 69.332 0.346 1.246 0.029 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.014 197.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 56.900 0.422 1.518 0.024 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.012 198.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 66.315 0.362 1.303 0.028 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (119 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.043 0.022 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 67.161 0.357 1.286 0.028 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.035 0.017 198.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 44.605 0.538 1.937 0.019 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.045 0.023 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 34.422 0.697 2.510 0.014 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (131 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.048 0.024 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 60.742 0.395 1.422 0.025 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.035 0.017 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 44.646 0.538 1.935 0.019 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 59.472 0.404 1.453 0.025 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (127 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.071 0.036 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 41.280 0.581 2.093 0.017 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.040 0.020 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 38.779 0.619 2.228 0.016 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.052 0.026 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 29.793 0.806 2.900 0.012 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (153 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.056 0.028 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 52.325 0.459 1.651 0.022 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.030 0.015 197.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 52.118 0.460 1.658 0.022 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.015 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 52.339 0.459 1.651 0.022 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (170 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.072 0.036 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 40.866 0.587 2.114 0.017 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.076 0.038 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 20.398 1.177 4.236 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.054 0.027 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 28.535 0.841 3.028 0.012 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (462 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.059 0.030 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.484 0.485 1.746 0.021 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.059 0.030 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 26.082 0.920 3.313 0.011 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.069 0.035 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 22.325 1.075 3.870 0.009 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (192 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.099 0.050 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 29.524 0.813 2.926 0.012 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.063 0.032 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 24.594 0.976 3.513 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.148 0.074 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 10.501 2.286 8.228 0.004 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (268 ms) 78: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (1626 ms total) 78: 78: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.021 0.010 198.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 141.068 0.170 0.612 0.020 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.028 0.014 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 54.845 0.438 1.575 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.019 0.010 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 79.411 0.302 1.088 0.011 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (65 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 111.875 0.215 0.772 0.016 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.022 0.011 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 70.415 0.341 1.227 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.018 0.009 198.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 84.696 0.283 1.020 0.012 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (63 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.015 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 99.169 0.242 0.871 0.014 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.021 0.011 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 73.234 0.328 1.180 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.018 0.009 198.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 87.795 0.273 0.984 0.012 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (63 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.015 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 95.601 0.251 0.904 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 60.575 0.396 1.426 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 46.039 0.521 1.877 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (75 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.038 0.019 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 76.877 0.312 1.124 0.011 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 59.545 0.403 1.451 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.014 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 53.631 0.448 1.611 0.007 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (76 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.015 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 101.025 0.238 0.855 0.014 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.028 0.014 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 56.014 0.428 1.542 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.014 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 56.601 0.424 1.526 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (73 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.043 0.022 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 67.578 0.355 1.279 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.015 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 52.938 0.453 1.632 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 47.650 0.504 1.813 0.007 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (84 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.016 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 94.287 0.255 0.916 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.013 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 58.173 0.413 1.485 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.022 0.011 198.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 71.143 0.337 1.214 0.010 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (70 ms) 78: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (574 ms total) 78: 78: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 78: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.030 0.015 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 97.213 0.247 0.889 0.014 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.015 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 52.537 0.457 1.645 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.028 0.014 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 55.388 0.433 1.560 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (75 ms) 78: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 91.892 0.261 0.940 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.014 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 56.763 0.423 1.522 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.304 0.530 1.907 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (77 ms) 78: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (152 ms total) 78: 78: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.028 0.014 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 102.800 0.233 0.840 0.014 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.014 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 57.459 0.418 1.504 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.933 0.523 1.881 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (76 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.035 0.018 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 83.755 0.287 1.032 0.012 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.030 0.015 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 52.037 0.461 1.660 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.014 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 54.030 0.444 1.599 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (77 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.015 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 94.999 0.253 0.909 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 59.650 0.402 1.448 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.015 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 50.307 0.477 1.717 0.007 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (74 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.015 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 100.096 0.240 0.863 0.014 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 48.521 0.495 1.781 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.013 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 58.099 0.413 1.487 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (74 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.033 0.016 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 90.005 0.267 0.960 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.033 0.017 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 46.349 0.518 1.864 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.011 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 68.474 0.350 1.262 0.010 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (74 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.033 0.017 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 87.553 0.274 0.987 0.012 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 47.808 0.502 1.807 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.016 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.642 0.483 1.740 0.007 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (79 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 78: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.015 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 99.586 0.241 0.868 0.014 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.113 0.489 1.759 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.014 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 56.475 0.425 1.530 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (75 ms) 78: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (532 ms total) 78: 78: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 78: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: MTTK coupling is deprecated and will soon be removed 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: MTTK coupling is deprecated and will soon be removed 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.035 0.018 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 82.875 0.290 1.043 0.012 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.016 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.544 0.484 1.744 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.039 0.019 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 39.947 0.601 2.163 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (85 ms) 78: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (85 ms total) 78: 78: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 78: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'FirstWaterMolecule' has 3 atoms 78: Pull group 2 'SecondWaterMolecule' has 3 atoms 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 2 78: 2 3 5 1.112 nm 1.000 nm 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'FirstWaterMolecule' has 3 atoms 78: Pull group 2 'SecondWaterMolecule' has 3 atoms 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 2 78: 2 3 5 1.112 nm 1.000 nm 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.042 0.021 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 69.101 0.347 1.250 0.005 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.097 0.049 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 15.938 1.506 5.421 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.046 0.023 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 33.499 0.716 2.579 0.002 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (128 ms) 78: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'FirstWaterMolecule' has 3 atoms 78: Pull group 2 'SecondWaterMolecule' has 3 atoms 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 2 78: 2 3 5 1.112 nm 1.000 nm 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'FirstWaterMolecule' has 3 atoms 78: Pull group 2 'SecondWaterMolecule' has 3 atoms 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 2 78: 2 3 5 1.112 nm 1.000 nm 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.056 0.028 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 52.793 0.455 1.637 0.004 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.047 0.023 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 33.195 0.723 2.603 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 44.961 0.534 1.922 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (103 ms) 78: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (231 ms total) 78: 78: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 78: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: Setting the AWH bias MC random seed to -9470498 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'C_&_r_1' has 1 atoms 78: Pull group 2 'N_&_r_2' has 1 atoms 78: Pull group 3 'CA' has 1 atoms 78: Pull group 4 'C_&_r_2' has 1 atoms 78: Pull group 5 'N_&_r_3' has 1 atoms 78: Number of degrees of freedom in T-Coupling group System is 51.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 1 0 78: 2 1 0 179.098 deg 0.000 deg 78: 2 1 0 78: 3 1 0 158.667 deg 0.000 deg 78: 78: There were 2 NOTEs 78: Setting the AWH bias MC random seed to -1191970897 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'C_&_r_1' has 1 atoms 78: Pull group 2 'N_&_r_2' has 1 atoms 78: Pull group 3 'CA' has 1 atoms 78: Pull group 4 'C_&_r_2' has 1 atoms 78: Pull group 5 'N_&_r_3' has 1 atoms 78: Number of degrees of freedom in T-Coupling group System is 51.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 1 0 78: 2 1 0 179.098 deg 0.000 deg 78: 2 1 0 78: 3 1 0 158.667 deg 0.000 deg 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.059 0.029 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.828 0.482 1.734 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.057 0.029 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 26.939 0.891 3.207 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.051 0.026 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 30.145 0.796 2.866 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (181 ms) 78: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: Setting the AWH bias MC random seed to -323264577 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'C_&_r_1' has 1 atoms 78: Pull group 2 'N_&_r_2' has 1 atoms 78: Pull group 3 'CA' has 1 atoms 78: Pull group 4 'C_&_r_2' has 1 atoms 78: Pull group 5 'N_&_r_3' has 1 atoms 78: Number of degrees of freedom in T-Coupling group System is 51.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 1 0 78: 2 1 0 179.098 deg 0.000 deg 78: 2 1 0 78: 3 1 0 158.667 deg 0.000 deg 78: 78: There were 2 NOTEs 78: Setting the AWH bias MC random seed to -1078390913 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'C_&_r_1' has 1 atoms 78: Pull group 2 'N_&_r_2' has 1 atoms 78: Pull group 3 'CA' has 1 atoms 78: Pull group 4 'C_&_r_2' has 1 atoms 78: Pull group 5 'N_&_r_3' has 1 atoms 78: Number of degrees of freedom in T-Coupling group System is 51.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 1 0 78: 2 1 0 179.098 deg 0.000 deg 78: 2 1 0 78: 3 1 0 158.667 deg 0.000 deg 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.057 0.029 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 51.454 0.466 1.679 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.067 0.034 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 23.140 1.037 3.734 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.035 0.017 198.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 44.549 0.539 1.939 0.011 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (172 ms) 78: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (354 ms total) 78: 78: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 78: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.053 0.026 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 55.611 0.432 1.554 0.023 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.058 0.029 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 26.589 0.903 3.249 0.011 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.036 0.018 197.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 42.550 0.564 2.031 0.018 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (178 ms) 78: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (178 ms total) 78: 78: [----------] 3 tests from Checking/InitialConstraintsTest 78: [ RUN ] Checking/InitialConstraintsTest.Works/0 78: Number of degrees of freedom in T-Coupling group rest is 11.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 1141.954 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 1 steps, 0.0 ps. 78: Setting the LD random seed to 1879012798 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 12.984 1.848 6.655 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (27 ms) 78: [ RUN ] Checking/InitialConstraintsTest.Works/1 78: Number of degrees of freedom in T-Coupling group rest is 11.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 1141.954 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 1 steps, 0.0 ps. 78: Setting the LD random seed to -571626506 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.024 0.012 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.542 1.650 5.942 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (25 ms) 78: [ RUN ] Checking/InitialConstraintsTest.Works/2 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 78: Integrator method md-vv-avek is implemented primarily for validation 78: purposes; for molecular dynamics, you should probably be using md or 78: md-vv 78: 78: Number of degrees of freedom in T-Coupling group rest is 11.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 78: NVE simulation: will use the initial temperature of 1141.954 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 1 steps, 0.0 ps. 78: Setting the LD random seed to -134303761 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.022 0.011 198.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 15.931 1.507 5.423 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (24 ms) 78: [----------] 3 tests from Checking/InitialConstraintsTest (77 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 76 tests from 13 test suites ran. (7753 ms total) 78: [ PASSED ] 76 tests. 78/103 Test #78: MdrunIOTests .............................. Passed 7.79 sec test 79 Start 79: MdrunTestsOneRank 79: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" 79: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 31 tests from 9 test suites. 79: [----------] Global test environment set-up. 79: [----------] 2 tests from AwhTest 79: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (10) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 20 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.079 0.040 198.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 45.474 0.528 1.900 0.012 79: [ OK ] AwhTest.SingleBiasMultiDimCanRun (87 ms) 79: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (10) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 20 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.048 0.024 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 74.913 0.320 1.153 0.019 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.017 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 108.575 0.221 0.796 0.028 79: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (98 ms) 79: [----------] 2 tests from AwhTest (186 ms total) 79: 79: [----------] 1 test from CompelTest 79: [ RUN ] CompelTest.SwapCanRun 79: Generating 1-4 interactions: fudge = 0.5 79: Split0 group 'Ch0' contains 83 atoms. 79: Split1 group 'Ch1' contains 83 atoms. 79: Solvent group 'SOL' contains 11931 atoms. 79: Swap group 'NA+' contains 19 atoms. 79: Swap group 'CL-' contains 19 atoms. 79: Number of degrees of freedom in T-Coupling group System is 27869.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 79: Removing center of mass motion in the presence of position restraints 79: might cause artifacts. When you are using position restraints to 79: equilibrate a macro-molecule, the artifacts are usually negligible. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Update groups can not be used for this system because there are three or more consecutively coupled constraints 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: SWAP: Determining initial numbers of ions per compartment. 79: SWAP: Setting pointers for checkpoint writing 79: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 79: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 79: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 79: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 79: starting mdrun 'Channel_coco in octane membrane' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to 1807478359 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein' 79: 79: turning all bonds into constraints... 79: 79: Excluding 3 bonded neighbours molecule type 'OCT' 79: 79: turning all bonds into constraints... 79: 79: Excluding 1 bonded neighbours molecule type 'NA' 79: 79: turning all bonds into constraints... 79: 79: Excluding 1 bonded neighbours molecule type 'CL' 79: 79: turning all bonds into constraints... 79: 79: Excluding 3 bonded neighbours molecule type 'Protein' 79: 79: Excluding 3 bonded neighbours molecule type 'OCT' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 1 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 12 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 1.029 0.515 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 2.014 11.914 171.568 0.081 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 79: 79: Update groups can not be used for this system because there are three or more consecutively coupled constraints 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: SWAP: Setting pointers for checkpoint writing 79: SWAP: Copying channel fluxes from checkpoint file data 79: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 79: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 79: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 79: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 79: starting mdrun 'Channel_coco in octane membrane' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.878 0.439 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 2.362 10.162 146.329 0.094 79: [ OK ] CompelTest.SwapCanRun (2135 ms) 79: [----------] 1 test from CompelTest (2135 ms total) 79: 79: [----------] 6 tests from BondedInteractionsTest 79: [ RUN ] BondedInteractionsTest.NormalBondWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 2 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 18 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 184.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 246.187 0.097 0.351 0.011 79: Setting the LD random seed to -538971715 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.NormalBondWorks (13 ms) 79: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 2 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 16 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 184.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 272.472 0.088 0.317 0.013 79: Setting the LD random seed to -2013333201 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.TabulatedBondWorks (15 ms) 79: [ RUN ] BondedInteractionsTest.NormalAngleWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 4 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 15 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 185.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 292.957 0.082 0.295 0.014 79: Setting the LD random seed to 905372591 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.NormalAngleWorks (11 ms) 79: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 4 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 15 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 183.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 292.013 0.082 0.296 0.014 79: Setting the LD random seed to -269484038 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (12 ms) 79: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 4 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 23 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 189.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 199.553 0.120 0.433 0.009 79: Setting the LD random seed to -29497617 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.NormalDihedralWorks (11 ms) 79: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 4 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 14 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 185.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 290.841 0.083 0.297 0.013 79: Setting the LD random seed to -8407441 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (14 ms) 79: [----------] 6 tests from BondedInteractionsTest (80 ms total) 79: 79: [----------] 2 tests from BoxDeformationTest 79: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (10) 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Number of degrees of freedom in T-Coupling group rest is 33.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 0 steps, 0.0 ps. 79: 79: NOTE: 16 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 165.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 461.935 0.052 0.374 0.032 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -68158469 79: 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Setting gen_seed to -92569907 79: 79: Velocities were taken from a Maxwell distribution at 0 K 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (14 ms) 79: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (10) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group rest is 1293.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Setting the LD random seed to -1568669697 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 79: 79: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 79: 79: Estimate for the relative computational load of the PME mesh part: 0.09 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.216 0.108 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 33.622 0.714 5.139 0.126 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (996 ms) 79: [----------] 2 tests from BoxDeformationTest (1010 ms total) 79: 79: [----------] 1 test from PositionRestraintCommTest 79: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (10) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 79: 13489 atoms are not part of any of the VCM groups 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 79: 13489 atoms are not part of any center of mass motion removal group. 79: This may lead to artifacts. 79: In most cases one should use one group for the whole system. 79: 79: Number of degrees of freedom in T-Coupling group System is 29527.73 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 79: Removing center of mass motion in the presence of position restraints 79: might cause artifacts. When you are using position restraints to 79: equilibrate a macro-molecule, the artifacts are usually negligible. 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Channel_coco in octane membrane' 79: 10 steps, 0.0 ps. 79: Setting the LD random seed to -165899 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein' 79: 79: Excluding 3 bonded neighbours molecule type 'OCT' 79: 79: Excluding 1 bonded neighbours molecule type 'NA' 79: 79: Excluding 1 bonded neighbours molecule type 'CL' 79: 79: Excluding 3 bonded neighbours molecule type 'Protein' 79: 79: Excluding 3 bonded neighbours molecule type 'OCT' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/OctaneSandwich.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: Chain0: 2.207 2.168 7.330 79: Chain1: 2.228 2.186 2.401 79: Chain0: 2.207 2.168 7.330 79: Chain1: 2.228 2.186 2.401 79: 79: This run will generate roughly 1 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 1.687 0.844 200.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 2.253 10.654 76.708 0.180 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (1954 ms) 79: [----------] 1 test from PositionRestraintCommTest (1954 ms total) 79: 79: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 79: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 3 [file ala.top, line 256]: 79: For energy conservation with LINCS, lincs_iter should be 2 or larger. 79: 79: 79: Number of degrees of freedom in T-Coupling group rest is 54.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'UNNAMED in water' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to -148931093 79: 79: Generated 2211 of the 2211 non-bonded parameter combinations 79: 79: Generated 2211 of the 2211 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 79: 79: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 79: 79: Estimate for the relative computational load of the PME mesh part: 0.93 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.034 0.017 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 25.006 0.960 3.455 0.007 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 3 [file ala.top, line 256]: 79: For energy conservation with LINCS, lincs_iter should be 2 or larger. 79: 79: 79: Number of degrees of freedom in T-Coupling group rest is 54.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'UNNAMED in water' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to -33572429 79: 79: Generated 2211 of the 2211 non-bonded parameter combinations 79: 79: Generated 2211 of the 2211 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 79: 79: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 79: 79: Estimate for the relative computational load of the PME mesh part: 0.93 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.039 0.020 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 22.092 1.086 3.911 0.006 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 79: 79: 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (123 ms) 79: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 3 [file ala.top, line 256]: 79: For energy conservation with LINCS, lincs_iter should be 2 or larger. 79: 79: 79: Number of degrees of freedom in T-Coupling group rest is 54.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'UNNAMED in water' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to -373297217 79: 79: Generated 2211 of the 2211 non-bonded parameter combinations 79: 79: Generated 2211 of the 2211 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 79: 79: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 79: 79: Estimate for the relative computational load of the PME mesh part: 0.93 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.046 0.023 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 18.787 1.277 4.599 0.005 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 3 [file ala.top, line 256]: 79: For energy conservation with LINCS, lincs_iter should be 2 or larger. 79: 79: 79: Number of degrees of freedom in T-Coupling group rest is 54.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'UNNAMED in water' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to 569454509 79: 79: Generated 2211 of the 2211 non-bonded parameter combinations 79: 79: Generated 2211 of the 2211 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 79: 79: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 79: 79: Estimate for the relative computational load of the PME mesh part: 0.93 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.030 0.015 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 28.479 0.843 3.034 0.008 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 79: 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (105 ms) 79: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (229 ms total) 79: 79: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 79: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to -8390169 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.056 0.028 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 15.360 1.562 5.625 0.001 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to -671621441 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.036 0.018 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 24.157 0.994 3.577 0.002 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 79: 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (76 ms) 79: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (76 ms total) 79: 79: [----------] 12 tests from FreezeWorks/FreezeGroupTest 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 246.451 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.028 0.014 198.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 54.954 0.437 1.572 0.014 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (43 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 246.451 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.033 0.016 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 47.487 0.505 1.819 0.012 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (44 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 246.451 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.039 0.019 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 39.944 0.601 2.163 0.010 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (48 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 246.451 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.040 0.020 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 39.103 0.614 2.210 0.010 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (49 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 79: NVE simulation: will use the initial temperature of 246.451 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.088 0.044 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 17.721 1.354 4.876 0.005 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (72 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 79: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 79: Parrinello-Rahman is not implemented in md-vv. 79: 79: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.063 0.032 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 24.511 0.979 3.525 0.006 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (67 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.045 0.023 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 34.540 0.695 2.501 0.009 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (59 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.043 0.022 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 35.808 0.670 2.413 0.009 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (58 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.051 0.026 199.3 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 30.475 0.788 2.835 0.008 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (107 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.046 0.023 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 33.477 0.717 2.581 0.009 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (105 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.034 0.017 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 45.204 0.531 1.911 0.012 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (98 ms) 79: [----------] 12 tests from FreezeWorks/FreezeGroupTest (756 ms total) 79: 79: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 79: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 79: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: Net Acceleration in X direction, will not be corrected 79: Net Acceleration in Y direction, will not be corrected 79: Net Acceleration in Z direction, will not be corrected 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to 922408827 79: 79: Velocities were taken from a Maxwell distribution at 0 K 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.041 0.020 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 76.026 0.316 2.273 0.003 79: 79: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (35 ms) 79: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 79: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 79: Net Acceleration in X direction, will not be corrected 79: Net Acceleration in Y direction, will not be corrected 79: Net Acceleration in Z direction, will not be corrected 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because verlet-buffer-tolerance is not set or used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -69077387 79: 79: Velocities were taken from a Maxwell distribution at 0 K 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.043 0.022 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 71.622 0.335 2.413 0.002 79: 79: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (35 ms) 79: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 79: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: Net Acceleration in X direction, will not be corrected 79: Net Acceleration in Y direction, will not be corrected 79: Net Acceleration in Z direction, will not be corrected 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -604226579 79: 79: Velocities were taken from a Maxwell distribution at 0 K 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 11 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.080 0.040 199.6 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 38.713 0.620 4.464 0.001 79: 79: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (58 ms) 79: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 79: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 79: Net Acceleration in X direction, will not be corrected 79: Net Acceleration in Y direction, will not be corrected 79: Net Acceleration in Z direction, will not be corrected 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 79: Can not increase nstlist because verlet-buffer-tolerance is not set or used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -679710817 79: 79: Velocities were taken from a Maxwell distribution at 0 K 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.035 0.017 199.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 88.873 0.270 1.944 0.003 79: 79: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (30 ms) 79: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (160 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 31 tests from 9 test suites ran. (6730 ms total) 79: [ PASSED ] 30 tests. 79: [ SKIPPED ] 1 test, listed below: 79: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 79/103 Test #79: MdrunTestsOneRank ......................... Passed 6.76 sec test 80 Start 80: MdrunTestsTwoRanks 80: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" 80: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 31 tests from 9 test suites. 80: [----------] Global test environment set-up. 80: [----------] 2 tests from AwhTest 80: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 2 MPI threads 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 11.8%. 80: The balanceable part of the MD step is 52%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 6.2%. 80: 80: NOTE: 6.2 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.470 0.118 397.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 15.346 1.564 5.630 0.004 80: [ OK ] AwhTest.SingleBiasMultiDimCanRun (170 ms) 80: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 34.4%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 14.7%. 80: 80: NOTE: 14.7 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 16 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 5.458 1.380 395.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.315 18.254 65.714 0.000 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 33.1%. 80: The balanceable part of the MD step is 45%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 15.0%. 80: 80: NOTE: 15.0 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 16 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 5.042 1.276 395.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.422 16.878 60.761 0.000 80: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (4032 ms) 80: [----------] 2 tests from AwhTest (4204 ms total) 80: 80: [----------] 1 test from CompelTest 80: [ RUN ] CompelTest.SwapCanRun 80: Generating 1-4 interactions: fudge = 0.5 80: Split0 group 'Ch0' contains 83 atoms. 80: Split1 group 'Ch1' contains 83 atoms. 80: Solvent group 'SOL' contains 11931 atoms. 80: Swap group 'NA+' contains 19 atoms. 80: Swap group 'CL-' contains 19 atoms. 80: Number of degrees of freedom in T-Coupling group System is 27869.00 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: SWAP: Determining initial numbers of ions per compartment. 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 2 steps, 0.0 ps. 80: Setting the LD random seed to -83952657 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning all bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.3%. 80: The balanceable part of the MD step is 40%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.3%. 80: 80: 80: NOTE: 26 % of the run time was spent in domain decomposition, 80: 6 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 6.462 1.628 396.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.637 37.683 542.642 0.025 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 80: 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Copying channel fluxes from checkpoint file data 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 4.096 1.040 393.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.997 24.072 346.637 0.040 80: [ OK ] CompelTest.SwapCanRun (5456 ms) 80: [----------] 1 test from CompelTest (5456 ms total) 80: 80: [----------] 6 tests from BondedInteractionsTest 80: [ RUN ] BondedInteractionsTest.NormalBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 79 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.937 0.246 380.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.351 68.393 246.213 0.000 80: Setting the LD random seed to -1075858180 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalBondWorks (814 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 78 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.969 0.254 381.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.340 70.617 254.223 0.000 80: Setting the LD random seed to -1493270529 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedBondWorks (823 ms) 80: [ RUN ] BondedInteractionsTest.NormalAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 77 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.959 0.252 380.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.343 69.943 251.795 0.000 80: Setting the LD random seed to -271079562 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalAngleWorks (827 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 80 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.921 0.242 380.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.357 67.283 242.219 0.000 80: Setting the LD random seed to 1048332022 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (847 ms) 80: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 81 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.954 0.251 380.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.345 69.602 250.566 0.000 80: Setting the LD random seed to -1083213925 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalDihedralWorks (831 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 79 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 7 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.954 0.247 387.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.350 68.490 246.562 0.000 80: Setting the LD random seed to -2108545 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (824 ms) 80: [----------] 6 tests from BondedInteractionsTest (4971 ms total) 80: 80: [----------] 2 tests from BoxDeformationTest 80: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Argon' 80: 0 steps, 0.0 ps. 80: 80: NOTE: 48 % of the run time was spent in domain decomposition, 80: 8 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 22 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.370 0.108 342.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.601 14.993 107.949 0.000 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1085543444 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Setting gen_seed to 2003378107 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (692 ms) 80: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group rest is 1293.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 20 steps, 0.0 ps. 80: Setting the LD random seed to 2147434430 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 80: 80: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 80: 80: Estimate for the relative computational load of the PME mesh part: 0.09 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB got disabled because it was unsuitable to use. 80: Average load imbalance: 31.3%. 80: The balanceable part of the MD step is 13%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 3.9%. 80: 80: 80: NOTE: 11 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 11.520 2.896 397.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.253 19.153 137.902 0.005 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (4432 ms) 80: [----------] 2 tests from BoxDeformationTest (5125 ms total) 80: 80: [----------] 1 test from PositionRestraintCommTest 80: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any of the VCM groups 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any center of mass motion removal group. 80: This may lead to artifacts. 80: In most cases one should use one group for the whole system. 80: 80: Number of degrees of freedom in T-Coupling group System is 29527.73 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Channel_coco in octane membrane' 80: 10 steps, 0.0 ps. 80: Setting the LD random seed to 1608447960 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/OctaneSandwich.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 6.704 1.692 396.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.123 21.362 153.810 0.090 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (3352 ms) 80: [----------] 1 test from PositionRestraintCommTest (3353 ms total) 80: 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 2143055838 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.93 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 9 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.333 0.599 389.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.721 33.286 119.830 0.000 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 1272315902 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.93 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 11 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.934 0.499 387.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.865 27.743 99.873 0.000 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 80: 80: 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (2571 ms) 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 1811543919 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.93 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 9 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.240 0.576 388.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.750 31.997 115.188 0.000 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -941711691 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.93 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 15 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 8 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.728 0.448 385.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.964 24.885 89.588 0.000 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (2466 ms) 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (5038 ms total) 80: 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -1789150733 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 12 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.612 0.419 384.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.031 23.282 83.816 0.000 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 1056964451 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 14 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 12 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.536 0.400 384.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.080 22.220 79.990 0.000 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (2085 ms) 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (2086 ms total) 80: 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 41.0%. 80: The balanceable part of the MD step is 37%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 15.3%. 80: 80: NOTE: 15.3 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 20 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 14 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.082 0.536 388.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.451 16.542 59.549 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (1186 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 41.3%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 16.1%. 80: 80: NOTE: 16.1 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 20 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 14 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.243 0.576 389.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.350 17.776 63.994 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (1211 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 33.1%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 13.6%. 80: 80: NOTE: 13.6 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 19 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 14 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.165 0.556 389.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.399 17.159 61.773 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (1215 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 28.3%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 12.2%. 80: 80: NOTE: 12.2 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 19 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 20 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.480 0.636 390.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.223 19.628 70.661 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (1284 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 23.3%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 11.8%. 80: 80: NOTE: 11.8 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 15 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.737 0.700 391.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.111 21.602 77.769 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (1359 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 80: Parrinello-Rahman is not implemented in md-vv. 80: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 15 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.794 0.464 386.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.676 14.318 51.545 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (1131 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 13 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.914 0.492 389.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.581 15.183 54.658 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (1151 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 16 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.938 0.500 387.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.555 15.430 55.548 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (1155 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 16 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.810 0.472 383.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.648 14.566 52.436 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (1219 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 16 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.828 0.472 387.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.648 14.567 52.442 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (1207 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 13 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 13 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.633 0.424 385.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.834 13.084 47.104 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (1164 ms) 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest (13291 ms total) 80: 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -41976131 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 13.4%. 80: The balanceable part of the MD step is 36%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 4.8%. 80: 80: 80: NOTE: 19 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 13 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.096 0.540 388.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 2.880 8.332 59.992 0.000 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (1116 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 2136993182 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 14.0%. 80: The balanceable part of the MD step is 37%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 5.2%. 80: 80: NOTE: 5.2 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 20 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 11 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.144 0.552 388.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 2.818 8.518 61.327 0.000 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (1119 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 2011168469 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 7.5%. 80: The balanceable part of the MD step is 40%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 3.0%. 80: 80: 80: NOTE: 17 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 22 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.368 0.608 389.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 2.558 9.382 67.554 0.000 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (1195 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -1079608009 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 6.8%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.7%. 80: 80: 80: NOTE: 16 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 25 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.355 0.605 389.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 2.572 9.332 67.191 0.000 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (1196 ms) 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (4628 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 31 tests from 9 test suites ran. (48295 ms total) 80: [ PASSED ] 30 tests. 80: [ SKIPPED ] 1 test, listed below: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80/103 Test #80: MdrunTestsTwoRanks ........................ Passed 48.33 sec test 81 Start 81: MdrunSingleRankAlgorithmsTests 81: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 5 tests from 3 test suites. 81: [----------] Global test environment set-up. 81: [----------] 1 test from DispersionCorrectionTest 81: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 30.00 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 81: There are 9 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 81: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 81: 81: Update groups can not be used for this system because an incompatible virtual site type is used 81: 81: Using 1 MPI thread 81: Using 2 OpenMP threads 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine dipeptide in vacuo' 81: 200 steps, 0.4 ps. 81: Setting the LD random seed to -1362382357 81: 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Converted 3 Bonds with virtual sites to connections, 7 left 81: 81: Removed 18 Angles with virtual sites, 21 left 81: 81: Removed 10 Proper Dih.s with virtual sites, 44 left 81: 81: Converted 12 Constraints with virtual sites to connections, 0 left 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.113 0.057 199.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 612.948 0.039 0.282 0.103 81: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (121 ms) 81: [----------] 1 test from DispersionCorrectionTest (121 ms total) 81: 81: [----------] 1 test from OriresTest 81: [ RUN ] OriresTest.OriresCanRun 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 518.00 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There was 1 NOTE 81: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 81: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 81: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 81: 81: 81: Using 1 MPI thread 81: Using 2 OpenMP threads 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 81: 10 steps, 0.0 ps. 81: Setting the LD random seed to -4409499 81: 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/orires_1lvz.gro' 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.099 0.050 199.4 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 38.262 0.627 4.516 0.048 81: [ OK ] OriresTest.OriresCanRun (865 ms) 81: [----------] 1 test from OriresTest (865 ms total) 81: 81: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 81: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 81: Number of degrees of freedom in T-Coupling group rest is 10.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 2 OpenMP threads 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Dipoles' 81: 20 steps, 0.1 ps. 81: Setting the LD random seed to 1543355389 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Dipole' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 81: 81: Searching the wall atom type(s) 81: 81: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.040 0.020 198.8 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 227.674 0.105 0.949 0.004 81: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 81: 81: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (69 ms) 81: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 81: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 81: The supported numbers are > 1. 81: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 81: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 81: With epsilon_surface > 0 all molecules should be neutral. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 81: With epsilon_surface > 0 you can only use domain decomposition when there 81: are only small molecules with all bonds constrained (mdrun will check for 81: this). 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 2 OpenMP threads 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Dipoles' 81: 20 steps, 0.1 ps. 81: Setting the LD random seed to -1393295555 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Dipole' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 81: 81: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.039 0.020 199.1 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 232.459 0.103 0.929 0.004 81: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 81: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (47 ms) 81: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (117 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 5 tests from 3 test suites ran. (1151 ms total) 81: [ PASSED ] 5 tests. 81/103 Test #81: MdrunSingleRankAlgorithmsTests ............ Passed 1.18 sec test 82 Start 82: Minimize1RankTests 82: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/Minimize1RankTests.xml" 82: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 82: Test timeout computed to be: 600 82: [==========] Running 12 tests from 2 test suites. 82: [----------] Global test environment set-up. 82: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Steepest Descents: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Steepest Descents did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = -4.7990990e+01 82: Maximum force = 1.8629788e+02 on atom 13 82: Norm of force = 8.7721985e+01 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (889 ms) 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Polak-Ribiere Conjugate Gradients: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: F-max = 3.02331e+02 on atom 3 82: F-Norm = 1.18024e+02 82: 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = -5.5862488e+01 82: Maximum force = 4.2726025e+02 on atom 13 82: Norm of force = 1.8452452e+02 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (850 ms) 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 1 82: Number of degrees of freedom in T-Coupling group System is 22.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Steepest Descents: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Steepest Descents did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = 3.1937717e+02 82: Maximum force = 9.9988662e+03 on atom 9 82: Norm of force = 4.6166996e+03 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 82: 82: Generated 17396 of the 20503 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Glycine' 82: 82: turning H bonds into constraints... 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (227 ms) 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 1 82: 82: NOTE 2 [file glycine_vacuo.top, line 12]: 82: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 82: 82: Number of degrees of freedom in T-Coupling group System is 22.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Polak-Ribiere Conjugate Gradients: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: F-max = 2.41575e+04 on atom 10 82: F-Norm = 1.18451e+04 82: 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = 1.5174423e+02 82: Maximum force = 7.4208853e+03 on atom 9 82: Norm of force = 3.5692989e+03 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 82: 82: Generated 17396 of the 20503 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Glycine' 82: 82: turning H bonds into constraints... 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (220 ms) 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: 82: NOTE 2 [file unknown]: 82: You are using constraints on all bonds, whereas the forcefield has been 82: parametrized only with constraints involving hydrogen atoms. We suggest 82: using constraints = h-bonds instead, this will also improve performance. 82: 82: Number of degrees of freedom in T-Coupling group System is 23.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: Update groups can not be used for this system because an incompatible virtual site type is used 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Steepest Descents: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Steepest Descents did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = -1.5698413e+02 82: Maximum force = 4.5706589e+02 on atom 17 82: Norm of force = 1.8328245e+02 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 82: 82: turning all bonds into constraints... 82: 82: Cleaning up constraints and constant bonded interactions with virtual sites 82: 82: Removed 18 Angles with virtual sites, 21 left 82: 82: Removed 10 Proper Dih.s with virtual sites, 44 left 82: 82: Converted 15 Constraints with virtual sites to connections, 7 left 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (28 ms) 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: 82: NOTE 2 [file unknown]: 82: You are using constraints on all bonds, whereas the forcefield has been 82: parametrized only with constraints involving hydrogen atoms. We suggest 82: using constraints = h-bonds instead, this will also improve performance. 82: 82: 82: NOTE 3 [file unknown]: 82: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 82: 82: Number of degrees of freedom in T-Coupling group System is 23.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: Update groups can not be used for this system because an incompatible virtual site type is used 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Polak-Ribiere Conjugate Gradients: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: F-max = 1.06801e+03 on atom 28 82: F-Norm = 4.26917e+02 82: 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = -1.6941089e+02 82: Maximum force = 2.1827660e+02 on atom 17 82: Norm of force = 7.9209024e+01 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 82: 82: turning all bonds into constraints... 82: 82: Cleaning up constraints and constant bonded interactions with virtual sites 82: 82: Removed 18 Angles with virtual sites, 21 left 82: 82: Removed 10 Proper Dih.s with virtual sites, 44 left 82: 82: Converted 15 Constraints with virtual sites to connections, 7 left 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (30 ms) 82: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2247 ms total) 82: 82: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Steepest Descents: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: 82: writing lowest energy coordinates. 82: 82: Steepest Descents converged to Fmax < 10 in 1 steps 82: Potential Energy = -9.7425699e-01 82: Maximum force = 4.0132303e+00 on atom 1 82: Norm of force = 1.6383944e+00 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (13 ms) 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Polak-Ribiere Conjugate Gradients: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: F-max = 4.01323e+00 on atom 1 82: F-Norm = 1.63839e+00 82: 82: 82: writing lowest energy coordinates. 82: 82: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 82: Potential Energy = -9.9064207e-01 82: Maximum force = 2.5781615e+00 on atom 1 82: Norm of force = 1.0525300e+00 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (14 ms) 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Low-Memory BFGS Minimizer: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: Using 10 BFGS correction steps. 82: 82: F-max = 4.01323e+00 on atom 1 82: F-Norm = 1.63839e+00 82: 82: 82: writing lowest energy coordinates. 82: 82: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 82: Potential Energy = -9.9064207e-01 82: Maximum force = 2.5781615e+00 on atom 1 82: Norm of force = 1.0525300e+00 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (13 ms) 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 1 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Steepest Descents: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Steepest Descents did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = 3.1939697e+02 82: Maximum force = 9.9704258e+03 on atom 9 82: Norm of force = 4.6227543e+03 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 82: 82: Generated 17396 of the 20503 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Glycine' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (239 ms) 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 1 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Polak-Ribiere Conjugate Gradients: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: F-max = 2.41672e+04 on atom 10 82: F-Norm = 1.19357e+04 82: 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = 1.5625757e+02 82: Maximum force = 7.5018242e+03 on atom 9 82: Norm of force = 3.6139019e+03 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 82: 82: Generated 17396 of the 20503 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Glycine' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (220 ms) 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 82: 82: Generating 1-4 interactions: fudge = 1 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 82: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Low-Memory BFGS Minimizer: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: Using 10 BFGS correction steps. 82: 82: F-max = 2.41672e+04 on atom 10 82: F-Norm = 1.19357e+04 82: 82: 82: Energy minimization has stopped, but the forces have not converged to the 82: requested precision Fmax < 10 (which may not be possible for your system). It 82: stopped because the algorithm tried to make a new step whose size was too 82: small, or there was no change in the energy since last step. Either way, we 82: regard the minimization as converged to within the available machine 82: precision, given your starting configuration and EM parameters. 82: 82: Double precision normally gives you higher accuracy, but this is often not 82: needed for preparing to run molecular dynamics. 82: 82: writing lowest energy coordinates. 82: 82: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 82: but did not reach the requested Fmax < 10. 82: Potential Energy = 5.6111578e+02 82: Maximum force = 1.2685379e+04 on atom 10 82: Norm of force = 6.0643592e+03 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 82: 82: Generated 17396 of the 20503 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Glycine' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (221 ms) 82: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (722 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 12 tests from 2 test suites ran. (3002 ms total) 82: [ PASSED ] 12 tests. 82/103 Test #82: Minimize1RankTests ........................ Passed 3.03 sec test 83 Start 83: Minimize2RankTests 83: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/Minimize2RankTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 12 tests from 2 test suites. 83: [----------] Global test environment set-up. 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 83: Using 2 MPI threads 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -4.7991024e+01 83: Maximum force = 1.8629745e+02 on atom 13 83: Norm of force = 8.7721978e+01 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (820 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 3.02331e+02 on atom 3 83: F-Norm = 1.18024e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -5.5862568e+01 83: Maximum force = 4.2725784e+02 on atom 13 83: Norm of force = 1.8452377e+02 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2689 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.1937720e+02 83: Maximum force = 9.9988643e+03 on atom 9 83: Norm of force = 4.6166993e+03 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1427 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: 83: NOTE 2 [file glycine_vacuo.top, line 12]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41575e+04 on atom 10 83: F-Norm = 1.18451e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.5174437e+02 83: Maximum force = 7.4208867e+03 on atom 9 83: Norm of force = 3.5692983e+03 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1939 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.5698407e+02 83: Maximum force = 4.5706586e+02 on atom 17 83: Norm of force = 1.8328245e+02 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (1296 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: 83: NOTE 3 [file unknown]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 1.06801e+03 on atom 28 83: F-Norm = 4.26917e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.6941095e+02 83: Maximum force = 2.1827661e+02 on atom 17 83: Norm of force = 7.9209030e+01 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (2387 ms) 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (10561 ms total) 83: 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents converged to Fmax < 10 in 1 steps 83: Potential Energy = -9.7425699e-01 83: Maximum force = 4.0132303e+00 on atom 3 83: Norm of force = 1.6383944e+00 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (677 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 4.01323e+00 on atom 3 83: F-Norm = 1.63839e+00 83: 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 83: Potential Energy = -9.9064207e-01 83: Maximum force = 2.5781615e+00 on atom 3 83: Norm of force = 1.0525300e+00 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (838 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (8 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.1939667e+02 83: Maximum force = 9.9704229e+03 on atom 9 83: Norm of force = 4.6227537e+03 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1355 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41672e+04 on atom 10 83: F-Norm = 1.19357e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.5625768e+02 83: Maximum force = 7.5018237e+03 on atom 9 83: Norm of force = 3.6139019e+03 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1811 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (177 ms) 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (4870 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 12 tests from 2 test suites ran. (15463 ms total) 83: [ PASSED ] 12 tests. 83/103 Test #83: Minimize2RankTests ........................ Passed 15.50 sec test 84 Start 84: MdrunNonIntegratorTests 84: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 84: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 84: Test timeout computed to be: 600 84: [==========] Running 46 tests from 3 test suites. 84: [----------] Global test environment set-up. 84: [----------] 1 test from NonbondedBenchTest 84: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 84: System size: 3000 atoms 84: Cut-off radius: 1 nm 84: Number of threads: 1 84: Number of iterations: 1 84: Compute energies: no 84: Ewald excl. corr.: analytical 84: 84: Coulomb LJ comb. SIMD intmod. Mcycles Mcycles/it. pairs/cycle 84: total useful 84: Ewald all geom. no PotShift 0.047 0.0471 25.2580 13.3626 84: [ OK ] NonbondedBenchTest.BasicEndToEndTest (107 ms) 84: [----------] 1 test from NonbondedBenchTest (107 ms total) 84: 84: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.089 0.044 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 33.010 0.727 2.617 0.005 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 84: 84: trr version: GMX_trn_file (single precision) 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 16 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 192.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1826.985 0.013 0.047 0.254 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (63 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.015 0.008 198.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 191.151 0.126 0.452 0.027 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 15 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 192.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1864.022 0.013 0.046 0.259 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (25 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.013 0.006 197.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 227.580 0.105 0.380 0.032 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 16 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 192.7 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1796.091 0.013 0.048 0.249 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (24 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.012 0.006 197.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 238.515 0.101 0.362 0.033 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 16 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 192.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1836.243 0.013 0.047 0.255 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (24 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.087 0.044 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 33.721 0.712 2.562 0.006 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 17 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 193.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1782.579 0.013 0.048 0.309 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (868 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.088 0.044 199.7 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 33.524 0.716 2.577 0.006 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 16 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 192.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1813.540 0.013 0.048 0.315 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (860 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.088 0.044 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 33.345 0.720 2.591 0.006 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 16 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 193.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1560.829 0.015 0.055 0.271 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (878 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.089 0.044 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 33.118 0.725 2.609 0.006 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 30 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 194.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1412.332 0.017 0.061 0.245 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (873 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 84: NVE simulation: will use the initial temperature of 456.887 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 84: There are 9 non-linear virtual site constructions. Their contribution to 84: the energy error is approximated. In most cases this does not affect the 84: error significantly. 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Alanine dipeptide in vacuo' 84: 16 steps, 0.0 ps. 84: Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.034 0.017 198.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 85.554 0.281 1.010 0.029 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 13 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 194.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1057.431 0.023 0.082 0.355 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (56 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 456.887 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 84: There are 9 non-linear virtual site constructions. Their contribution to 84: the energy error is approximated. In most cases this does not affect the 84: error significantly. 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Alanine dipeptide in vacuo' 84: 16 steps, 0.0 ps. 84: Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.008 197.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 173.167 0.139 0.499 0.058 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 13 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 194.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1063.638 0.023 0.081 0.357 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (47 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 84: There are 9 non-linear virtual site constructions. Their contribution to 84: the energy error is approximated. In most cases this does not affect the 84: error significantly. 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 84: 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Alanine dipeptide in vacuo' 84: 16 steps, 0.0 ps. 84: Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.162 0.081 199.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 18.125 1.324 4.767 0.006 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 84: 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 13 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 194.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1014.256 0.024 0.085 0.340 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (275 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 84: There are 9 non-linear virtual site constructions. Their contribution to 84: the energy error is approximated. In most cases this does not affect the 84: error significantly. 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 84: 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Alanine dipeptide in vacuo' 84: 16 steps, 0.0 ps. 84: Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.032 0.016 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 90.947 0.264 0.950 0.031 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 84: 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 14 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 194.7 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1080.048 0.022 0.080 0.363 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (112 ms) 84: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (4111 ms total) 84: 84: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.055 0.028 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 53.356 0.450 1.619 0.022 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 185.3 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 714.686 0.034 0.121 0.298 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (69 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.047 0.024 199.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 61.541 0.390 1.404 0.026 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 708.848 0.034 0.122 0.295 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (66 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.026 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 57.076 0.420 1.514 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 12 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 184.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 796.148 0.030 0.109 0.332 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (65 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.026 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 57.259 0.419 1.509 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 51 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.044 0.022 198.7 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 66.558 0.361 1.298 0.028 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (90 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.042 0.021 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 69.671 0.344 1.240 0.029 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 185.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 732.968 0.033 0.118 0.305 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (62 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.042 0.021 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 69.364 0.346 1.246 0.029 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 708.521 0.034 0.122 0.295 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (63 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.043 0.022 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 68.184 0.352 1.267 0.028 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.4 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 746.286 0.032 0.116 0.311 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (63 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.026 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 57.577 0.417 1.501 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 185.3 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 780.415 0.031 0.111 0.325 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (65 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.042 0.021 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 69.013 0.348 1.252 0.029 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 12 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 185.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 820.537 0.029 0.105 0.342 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (61 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.059 0.030 199.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 49.400 0.486 1.749 0.021 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 10 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 185.7 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 741.793 0.032 0.116 0.309 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (71 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.043 0.021 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 68.351 0.351 1.264 0.028 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 742.240 0.032 0.116 0.309 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (62 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.063 0.031 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 46.746 0.513 1.848 0.019 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 10 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 185.4 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 736.649 0.033 0.117 0.307 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (73 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.059 0.029 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 49.885 0.481 1.732 0.021 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 184.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 813.280 0.030 0.106 0.339 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (70 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.053 0.027 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 55.075 0.436 1.569 0.023 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 755.901 0.032 0.114 0.315 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (67 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.050 0.025 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 58.140 0.413 1.486 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 184.3 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 815.541 0.029 0.106 0.340 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (65 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.058 0.029 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 50.660 0.474 1.705 0.021 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 185.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 798.211 0.030 0.108 0.333 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (69 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.044 0.022 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 65.844 0.364 1.312 0.027 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 756.365 0.032 0.114 0.315 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (64 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.044 0.022 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 66.449 0.361 1.300 0.028 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 185.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 824.711 0.029 0.105 0.344 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (62 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.044 0.022 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 66.177 0.363 1.306 0.028 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 13 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 184.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 799.143 0.030 0.108 0.333 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (62 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.056 0.028 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 52.352 0.458 1.650 0.022 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 10 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 692.824 0.035 0.125 0.289 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (69 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.046 0.023 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 63.291 0.379 1.365 0.026 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 185.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 755.994 0.032 0.114 0.315 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (65 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.045 0.022 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 65.344 0.367 1.322 0.027 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 750.926 0.032 0.115 0.313 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (75 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.050 0.025 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 57.964 0.414 1.491 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 738.769 0.032 0.117 0.308 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (88 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.060 0.030 199.3 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 48.731 0.493 1.773 0.020 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 12 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 182.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 792.665 0.030 0.109 0.330 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (92 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.052 0.026 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 56.364 0.426 1.533 0.023 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.4 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 727.171 0.033 0.119 0.303 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (89 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.026 199.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 56.825 0.422 1.520 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 184.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 722.820 0.033 0.120 0.301 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (87 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.054 0.027 199.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 53.996 0.444 1.600 0.022 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 742.598 0.032 0.116 0.309 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (90 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.049 0.025 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 59.856 0.401 1.443 0.025 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 186.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 736.913 0.033 0.117 0.307 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (87 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.075 0.038 199.4 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 38.918 0.617 2.220 0.016 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 183.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 727.085 0.033 0.119 0.303 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (101 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.043 0.021 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 68.342 0.351 1.264 0.028 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 12 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 185.3 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 794.300 0.030 0.109 0.331 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (93 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.042 0.021 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 68.926 0.348 1.254 0.029 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 185.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 735.945 0.033 0.117 0.307 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (84 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.042 0.021 198.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 69.618 0.345 1.241 0.029 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 12 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 185.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 796.972 0.030 0.108 0.332 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (82 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.050 0.025 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 58.248 0.412 1.483 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 185.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 726.057 0.033 0.119 0.303 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (88 ms) 84: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (2477 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 46 tests from 3 test suites ran. (6727 ms total) 84: [ PASSED ] 46 tests. 84/103 Test #84: MdrunNonIntegratorTests ................... Passed 6.76 sec test 85 Start 85: MdrunTpiTests 85: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunTpiTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 3 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 3 tests from Simple/TpiTest 85: [ RUN ] Simple/TpiTest.ReproducesOutput/0 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 1308.00 85: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 85: Using 1 MPI thread 85: Using 1 OpenMP thread 85: 85: 85: NOTE: Thread affinity was not set. 85: Reading frames from gro file '216 water molecules', 648 atoms. 85: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 85: Last frame 0 time 0.000 85: Generated 331705 of the 331705 non-bonded parameter combinations 85: 85: Generated 331705 of the 331705 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Excluding 3 bonded neighbours molecule type 'methane' 85: Analysing residue names: 85: There are: 216 Water residues 85: There are: 1 Other residues 85: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] Simple/TpiTest.ReproducesOutput/0 (932 ms) 85: [ RUN ] Simple/TpiTest.ReproducesOutput/1 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 1308.00 85: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 85: Using 1 MPI thread 85: Using 1 OpenMP thread 85: 85: 85: NOTE: Thread affinity was not set. 85: Reading frames from gro file '216 water molecules', 648 atoms. 85: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 85: Last frame 0 time 0.000 85: Generated 331705 of the 331705 non-bonded parameter combinations 85: 85: Generated 331705 of the 331705 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Excluding 3 bonded neighbours molecule type 'methane' 85: Analysing residue names: 85: There are: 216 Water residues 85: There are: 1 Other residues 85: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] Simple/TpiTest.ReproducesOutput/1 (897 ms) 85: [ RUN ] Simple/TpiTest.ReproducesOutput/2 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 1308.00 85: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 85: Using 1 MPI thread 85: Using 1 OpenMP thread 85: 85: 85: NOTE: Thread affinity was not set. 85: Reading frames from gro file '216 water molecules', 648 atoms. 85: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 85: Last frame 0 time 0.000 85: Generated 331705 of the 331705 non-bonded parameter combinations 85: 85: Generated 331705 of the 331705 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Excluding 3 bonded neighbours molecule type 'methane' 85: Analysing residue names: 85: There are: 216 Water residues 85: There are: 1 Other residues 85: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] Simple/TpiTest.ReproducesOutput/2 (909 ms) 85: [----------] 3 tests from Simple/TpiTest (2739 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 3 tests from 1 test suite ran. (2755 ms total) 85: [ PASSED ] 3 tests. 85/103 Test #85: MdrunTpiTests ............................. Passed 2.78 sec test 86 Start 86: MdrunMpiTests 86: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunMpiTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 16 tests from 2 test suites. 86: [----------] Global test environment set-up. 86: [----------] 4 tests from MimicTest 86: [ RUN ] MimicTest.OneQuantumMol 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 86: For a correct single-point energy evaluation with nsteps = 0, use 86: continuation = yes to avoid constraining the input coordinates. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 21.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 86: NVE simulation with an initial temperature of zero: will use a Verlet 86: buffer of 10%. Check your energy drift! 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 86: 86: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 86: Reading frame 0 time 0.000 Last frame 0 time 0.000 86: 86: NOTE: 11 % of the run time was spent in domain decomposition, 86: 5 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.004 0.001 386.4 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 88.995 0.270 0.971 0.012 86: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2076831130 86: 86: Generated 10 of the 10 non-bonded parameter combinations 86: 86: Generated 10 of the 10 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] MimicTest.OneQuantumMol (17 ms) 86: [ RUN ] MimicTest.AllQuantumMol 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 86: For a correct single-point energy evaluation with nsteps = 0, use 86: continuation = yes to avoid constraining the input coordinates. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 21.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 86: NVE simulation with an initial temperature of zero: will use a Verlet 86: buffer of 10%. Check your energy drift! 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 86: 86: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 86: Reading frame 0 time 0.000 Last frame 0 time 0.000 86: 86: NOTE: 81 % of the run time was spent in domain decomposition, 86: 2 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: NOTE: 6 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 1.007 0.264 381.8 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 0.328 73.229 263.625 0.000 86: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -5407329 86: 86: Generated 10 of the 10 non-bonded parameter combinations 86: 86: Generated 10 of the 10 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] MimicTest.AllQuantumMol (877 ms) 86: [ RUN ] MimicTest.TwoQuantumMol 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 86: For a correct single-point energy evaluation with nsteps = 0, use 86: continuation = yes to avoid constraining the input coordinates. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 21.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 86: NVE simulation with an initial temperature of zero: will use a Verlet 86: buffer of 10%. Check your energy drift! 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 86: 86: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 86: Reading frame 0 time 0.000 Last frame 0 time 0.000 86: 86: NOTE: 82 % of the run time was spent in domain decomposition, 86: 3 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: NOTE: 6 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 1.007 0.264 381.8 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 0.328 73.229 263.626 0.000 86: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1073873285 86: 86: Generated 10 of the 10 non-bonded parameter combinations 86: 86: Generated 10 of the 10 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] MimicTest.TwoQuantumMol (851 ms) 86: [ RUN ] MimicTest.BondCuts 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 86: For a correct single-point energy evaluation with nsteps = 0, use 86: continuation = yes to avoid constraining the input coordinates. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 66.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 86: NVE simulation: will use the initial temperature of 300.368 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 86: 86: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 86: Reading frame 0 time 0.000 Last frame 0 time 0.000 86: 86: NOTE: 77 % of the run time was spent in domain decomposition, 86: 3 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: NOTE: 7 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.963 0.253 381.0 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 0.342 70.189 252.679 0.000 86: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1048507773 86: 86: Generated 2211 of the 2211 non-bonded parameter combinations 86: 86: Generated 2211 of the 2211 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] MimicTest.BondCuts (844 ms) 86: [----------] 4 tests from MimicTest (2591 ms total) 86: 86: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 9.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 86: NVE simulation with an initial temperature of zero: will use a Verlet 86: buffer of 10%. Check your energy drift! 86: 86: 86: There was 1 NOTE 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 9.00 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 9.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 86: NVE simulation with an initial temperature of zero: will use a Verlet 86: buffer of 10%. Check your energy drift! 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: There were 2 NOTEs 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 9.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: There was 1 NOTE 86: Setting the LD random seed to -1613104203 86: 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 86: 86: This run will generate roughly 0 Mb of data 86: Setting the LD random seed to 1278863614 86: 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Setting the LD random seed to -538003745 86: 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 86: 86: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 1.00 86: 86: This run will generate roughly 0 Mb of data 86: Setting the LD random seed to 735563519 86: 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 86: 86: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 86: 86: Estimate for the relative computational load of the PME mesh part: 1.00 86: 86: This run will generate roughly 0 Mb of data 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: 86: Dynamic load balancing report: 86: DLB was off during the run due to low measured imbalance. 86: Average load imbalance: 1.8%. 86: The balanceable part of the MD step is 36%, load imbalance is computed from this. 86: Part of the total run time spent waiting due to load imbalance: 0.7%. 86: 86: 86: NOTE: 20 % of the run time was spent in domain decomposition, 86: 3 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: NOTE: 15 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 3.041 0.776 392.0 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 2.338 10.264 36.950 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (1374 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot have separate PME ranks when PME is not used 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot have separate PME ranks when PME is not used 86: Cannot use two separate PME ranks when there are less than four ranks total 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 86: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 86: 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: NOTE: 18 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 2.401 0.616 389.9 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 2.946 8.147 29.331 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (1202 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot have separate PME ranks when PME is not used 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot have separate PME ranks when PME is not used 86: Cannot use two separate PME ranks when there are less than four ranks total 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: 86: Dynamic load balancing report: 86: DLB was turned on during the run due to measured imbalance. 86: Average load imbalance: 18.8%. 86: The balanceable part of the MD step is 13%, load imbalance is computed from this. 86: Part of the total run time spent waiting due to load imbalance: 2.5%. 86: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 86: 86: 86: NOTE: 6 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 7.442 1.876 396.7 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 0.967 24.814 89.331 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (2543 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 2.049 0.528 388.2 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 3.437 6.983 25.138 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (927 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot use two separate PME ranks when there are less than four ranks total 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: NOTE: 6 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 6.929 1.748 396.4 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 1.038 23.121 83.235 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (2423 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 2.107 0.544 387.5 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 3.336 7.194 25.900 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (983 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot use two separate PME ranks when there are less than four ranks total 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 86: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (9458 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 16 tests from 2 test suites ran. (12151 ms total) 86: [ PASSED ] 10 tests. 86: [ SKIPPED ] 6 tests, listed below: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 86/103 Test #86: MdrunMpiTests ............................. Passed 12.18 sec test 87 Start 87: MdrunMultiSimTests 87: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 2 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 2 tests from InNvt/MultiSimTerminationTest 87: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 87: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 87: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 87: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 87: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 2 tests from 1 test suite ran. (16 ms total) 87: [ PASSED ] 2 tests. 87: 87: YOU HAVE 4 DISABLED TESTS 87: 87/103 Test #87: MdrunMultiSimTests ........................ Passed 0.04 sec test 88 Start 88: MdrunMultiSimReplexTests 88: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 1 test from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 88: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 88: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 88: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 1 test from 1 test suite ran. (15 ms total) 88: [ PASSED ] 1 test. 88: 88: YOU HAVE 4 DISABLED TESTS 88: 88/103 Test #88: MdrunMultiSimReplexTests .................. Passed 0.04 sec test 89 Start 89: MdrunMultiSimReplexEquivalenceTests 89: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 0 tests from 0 test suites. 89: [==========] 0 tests from 0 test suites ran. (0 ms total) 89: [ PASSED ] 0 tests. 89: 89: YOU HAVE 10 DISABLED TESTS 89: 89/103 Test #89: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.03 sec test 90 Start 90: MdrunMpi1RankPmeTests 90: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 19 tests from 1 test suite. 90: [----------] Global test environment set-up. 90: [----------] 19 tests from ReproducesEnergies/PmeTest 90: Number of degrees of freedom in T-Coupling group rest is 12.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 90: NVE simulation: will use the initial temperature of 1046.791 K for 90: determining the Verlet buffer size 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: There were 2 NOTEs 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 90: For a correct single-point energy evaluation with nsteps = 0, use 90: continuation = yes to avoid constraining the input coordinates. 90: 90: Number of degrees of freedom in T-Coupling group rest is 13.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 90: NVE simulation: will use the initial temperature of 966.268 K for 90: determining the Verlet buffer size 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: There were 3 NOTEs 90: Setting the LD random seed to -1682337985 90: 90: Generated 8 of the 10 non-bonded parameter combinations 90: 90: Excluding 2 bonded neighbours molecule type 'Methanol' 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 90: 90: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 90: 90: Estimate for the relative computational load of the PME mesh part: 1.00 90: 90: This run will generate roughly 0 Mb of data 90: Setting the LD random seed to -1367395362 90: 90: Generated 8 of the 10 non-bonded parameter combinations 90: 90: Excluding 2 bonded neighbours molecule type 'Methanol' 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 90: 90: Searching the wall atom type(s) 90: 90: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 90: 90: Estimate for the relative computational load of the PME mesh part: 1.00 90: 90: This run will generate roughly 0 Mb of data 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 90: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'spc-and-methanol' 90: 20 steps, 0.0 ps. 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.086 0.043 199.5 90: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 90: Performance: 42.144 0.569 2.050 0.003 90: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (63 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 90: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'spc-and-methanol' 90: 20 steps, 0.0 ps. 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.067 0.033 199.4 90: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 90: Performance: 54.338 0.442 1.590 0.004 90: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (44 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: it targets GPU execution of FFT work, which is not supported in the current build 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 90: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'spc-and-methanol' 90: 0 steps, 0.0 ps. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.008 0.004 194.5 90: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 90: Performance: 20.042 1.197 4.311 0.001 90: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (40 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: it targets GPU execution of FFT work, which is not supported in the current build 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: it targets GPU execution, but no compatible devices were detected 90: it targets GPU execution of FFT work, which is not supported in the current build 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: it targets GPU execution, but no compatible devices were detected 90: it targets GPU execution of FFT work, which is not supported in the current build 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 90: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'spc-and-methanol' 90: 20 steps, 0.0 ps. 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.069 0.034 199.4 90: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 90: Performance: 52.735 0.455 1.638 0.004 90: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (45 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: it targets GPU execution of FFT work, which is not supported in the current build 90: PME GPU does not support: 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 90: [----------] 19 tests from ReproducesEnergies/PmeTest (197 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 19 tests from 1 test suite ran. (232 ms total) 90: [ PASSED ] 4 tests. 90: [ SKIPPED ] 15 tests, listed below: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 90/103 Test #90: MdrunMpi1RankPmeTests ..................... Passed 0.26 sec test 91 Start 91: MdrunMpi2RankPmeTests 91: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 91: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 19 tests from 1 test suite. 91: [----------] Global test environment set-up. 91: [----------] 19 tests from ReproducesEnergies/PmeTest 91: Number of degrees of freedom in T-Coupling group rest is 12.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 1046.791 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 2 NOTEs 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: For a correct single-point energy evaluation with nsteps = 0, use 91: continuation = yes to avoid constraining the input coordinates. 91: 91: Number of degrees of freedom in T-Coupling group rest is 13.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 966.268 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 3 NOTEs 91: Setting the LD random seed to -539721745 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: Setting the LD random seed to -153387393 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: Searching the wall atom type(s) 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: 91: Dynamic load balancing report: 91: DLB was off during the run due to low measured imbalance. 91: Average load imbalance: 7.0%. 91: The balanceable part of the MD step is 9%, load imbalance is computed from this. 91: Part of the total run time spent waiting due to load imbalance: 0.6%. 91: 91: 91: NOTE: 29 % of the run time was spent communicating energies, 91: you might want to increase some nst* mdp options 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.130 0.033 398.5 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 55.623 0.431 1.553 0.004 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (61 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: 91: Dynamic load balancing report: 91: DLB was turned on during the run due to measured imbalance. 91: Average load imbalance: 35.5%. 91: The balanceable part of the MD step is 19%, load imbalance is computed from this. 91: Part of the total run time spent waiting due to load imbalance: 6.7%. 91: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 91: 91: NOTE: 6.7 % of the available CPU time was lost due to load imbalance 91: in the domain decomposition. 91: You can consider manually changing the decomposition (option -dd); 91: e.g. by using fewer domains along the box dimension in which there is 91: considerable inhomogeneity in the simulated system. 91: 91: NOTE: 12 % of the run time was spent communicating energies, 91: you might want to increase some nst* mdp options 91: 91: Core t (s) Wall t (s) (%) 91: Time: 9.792 2.464 397.4 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 0.736 32.591 117.329 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (3140 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 0 steps, 0.0 ps. 91: 91: NOTE: 25 % of the run time was spent in domain decomposition, 91: 3 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: NOTE: 6 % of the run time was spent communicating energies, 91: you might want to increase some nst* mdp options 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.745 0.204 365.2 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 0.424 56.661 203.980 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (890 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 2.207 0.568 388.6 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 3.195 7.513 27.045 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (988 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 2.158 0.556 388.1 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 3.264 7.354 26.474 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (960 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 0 steps, 0.0 ps. 91: 91: NOTE: 11 % of the run time was spent in domain decomposition, 91: 0 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.129 0.048 269.8 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 1.802 13.315 47.935 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (503 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: 91: Dynamic load balancing report: 91: DLB was turned on during the run due to measured imbalance. 91: Average load imbalance: 32.9%. 91: The balanceable part of the MD step is 20%, load imbalance is computed from this. 91: Part of the total run time spent waiting due to load imbalance: 6.6%. 91: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 91: 91: NOTE: 6.6 % of the available CPU time was lost due to load imbalance 91: in the domain decomposition. 91: You can consider manually changing the decomposition (option -dd); 91: e.g. by using fewer domains along the box dimension in which there is 91: considerable inhomogeneity in the simulated system. 91: 91: NOTE: 13 % of the run time was spent communicating energies, 91: you might want to increase some nst* mdp options 91: 91: Core t (s) Wall t (s) (%) 91: Time: 9.872 2.484 397.4 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 0.730 32.856 118.283 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (3148 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [----------] 19 tests from ReproducesEnergies/PmeTest (9695 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 19 tests from 1 test suite ran. (9730 ms total) 91: [ PASSED ] 7 tests. 91: [ SKIPPED ] 12 tests, listed below: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91/103 Test #91: MdrunMpi2RankPmeTests ..................... Passed 9.76 sec test 92 Start 92: MdrunMpi4RankPmeTests 92: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "1" "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunMpi4RankPmeTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 19 tests from 1 test suite. 92: [----------] Global test environment set-up. 92: [----------] 19 tests from ReproducesEnergies/PmeTest 92: Number of degrees of freedom in T-Coupling group rest is 12.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 1046.791 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 2 NOTEs 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: For a correct single-point energy evaluation with nsteps = 0, use 92: continuation = yes to avoid constraining the input coordinates. 92: 92: Number of degrees of freedom in T-Coupling group rest is 13.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 966.268 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 3 NOTEs 92: Setting the LD random seed to -1118111489 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: Setting the LD random seed to -1214253961 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: Searching the wall atom type(s) 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 14.5%. 92: The balanceable part of the MD step is 5%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.8%. 92: 92: 92: NOTE: 36 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.126 0.032 398.3 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 57.465 0.418 1.504 0.004 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (69 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 20.8%. 92: The balanceable part of the MD step is 22%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 4.5%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: 92: 92: NOTE: 23 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 17.440 4.404 396.0 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.412 58.254 209.714 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (6006 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: NOTE: 32 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 13 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.393 0.392 355.2 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.220 108.973 392.302 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (2003 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 8.9%. 92: The balanceable part of the MD step is 66%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 5.8%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: Average PME mesh/force load: 0.106 92: Part of the total run time spent waiting due to PP/PME imbalance: 4.5 % 92: 92: NOTE: 5.8 % of the available CPU time was lost due to load imbalance 92: in the domain decomposition. 92: You can consider manually changing the decomposition (option -dd); 92: e.g. by using fewer domains along the box dimension in which there is 92: considerable inhomogeneity in the simulated system. 92: 92: NOTE: 12 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 32 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 8.256 2.116 390.2 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.857 27.989 100.761 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (3651 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 15.3%. 92: The balanceable part of the MD step is 59%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 9.0%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: Average PME mesh/force load: 0.102 92: Part of the total run time spent waiting due to PP/PME imbalance: 5.3 % 92: 92: NOTE: 9.0 % of the available CPU time was lost due to load imbalance 92: in the domain decomposition. 92: You can consider manually changing the decomposition (option -dd); 92: e.g. by using fewer domains along the box dimension in which there is 92: considerable inhomogeneity in the simulated system. 92: NOTE: 5.3 % performance was lost because the PME ranks 92: had less work to do than the PP ranks. 92: You might want to decrease the number of PME ranks 92: or decrease the cut-off and the grid spacing. 92: 92: 92: NOTE: 14 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 32 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 7.232 1.856 389.7 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.978 24.550 88.380 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (3364 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: NOTE: 43 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 15 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.736 0.228 322.9 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.379 63.329 227.986 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (1762 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 8.1%. 92: The balanceable part of the MD step is 23%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 1.9%. 92: 92: 92: NOTE: 23 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 17.678 4.464 396.0 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.406 59.048 212.571 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as single precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (5968 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [----------] 19 tests from ReproducesEnergies/PmeTest (22828 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 19 tests from 1 test suite ran. (22863 ms total) 92: [ PASSED ] 7 tests. 92: [ SKIPPED ] 12 tests, listed below: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92/103 Test #92: MdrunMpi4RankPmeTests ..................... Passed 22.89 sec test 93 Start 93: MdrunCoordinationBasicTests1Rank 93: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 93: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 93: Test timeout computed to be: 1920 93: [==========] Running 1 test from 1 test suite. 93: [----------] Global test environment set-up. 93: [----------] 1 test from BasicPropagators/PeriodicActionsTest 93: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: Setting nstcalcenergy (100) equal to nstenergy (1) 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: There were 2 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.045 0.045 99.8 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 32.432 0.740 2.664 0.005 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: Setting nstcalcenergy (100) equal to nstenergy (1) 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: There were 2 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.012 0.012 99.4 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 119.893 0.200 0.721 0.017 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: Setting nstcalcenergy (100) equal to nstenergy (4) 93: 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 93: setting nstcomm equal to nstcalcenergy for less overhead 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: COM removal frequency is set to (1). 93: Other settings require a global communication frequency of 4. 93: Note that this will require additional global communication steps, 93: which will reduce performance when using multiple ranks. 93: Consider setting nstcomm to a multiple of 4. 93: 93: 93: There were 4 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.005 0.005 98.8 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 276.607 0.087 0.312 0.038 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 93: setting nstcomm equal to nstcalcenergy for less overhead 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: COM removal frequency is set to (1). 93: Other settings require a global communication frequency of 100. 93: Note that this will require additional global communication steps, 93: which will reduce performance when using multiple ranks. 93: Consider setting nstcomm to a multiple of 100. 93: 93: 93: There were 3 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.006 0.006 98.9 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 228.644 0.105 0.378 0.032 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 93: setting nstcomm equal to nstcalcenergy for less overhead 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: COM removal frequency is set to (1). 93: Other settings require a global communication frequency of 100. 93: Note that this will require additional global communication steps, 93: which will reduce performance when using multiple ranks. 93: Consider setting nstcomm to a multiple of 100. 93: 93: 93: There were 3 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.006 0.006 98.8 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 249.336 0.096 0.347 0.035 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 93: setting nstcomm equal to nstcalcenergy for less overhead 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: COM removal frequency is set to (1). 93: Other settings require a global communication frequency of 100. 93: Note that this will require additional global communication steps, 93: which will reduce performance when using multiple ranks. 93: Consider setting nstcomm to a multiple of 100. 93: 93: 93: There were 3 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.006 0.006 98.8 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 241.374 0.099 0.358 0.034 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 93: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (161 ms) 93: [----------] 1 test from BasicPropagators/PeriodicActionsTest (161 ms total) 93: 93: [----------] Global test environment tear-down 93: [==========] 1 test from 1 test suite ran. (177 ms total) 93: [ PASSED ] 1 test. 93/103 Test #93: MdrunCoordinationBasicTests1Rank .......... Passed 0.20 sec test 94 Start 94: MdrunCoordinationBasicTests2Ranks 94: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 94: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 94: Test timeout computed to be: 1920 94: [==========] Running 1 test from 1 test suite. 94: [----------] Global test environment set-up. 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest 94: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.5%. 94: The balanceable part of the MD step is 57%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.9%. 94: 94: 94: NOTE: 45 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.033 0.016 198.5 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 89.605 0.268 0.964 0.012 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.5%. 94: The balanceable part of the MD step is 53%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.8%. 94: 94: 94: NOTE: 43 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.017 0.008 197.8 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 173.994 0.138 0.497 0.024 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 4. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 4. 94: 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.8%. 94: The balanceable part of the MD step is 51%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.9%. 94: 94: 94: NOTE: 44 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.019 0.010 198.1 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 152.454 0.157 0.567 0.021 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.5%. 94: The balanceable part of the MD step is 50%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.7%. 94: 94: 94: NOTE: 46 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.021 0.010 198.2 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 140.353 0.171 0.616 0.019 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.7%. 94: The balanceable part of the MD step is 51%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.8%. 94: 94: 94: NOTE: 46 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.022 0.011 198.2 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 134.241 0.179 0.644 0.019 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.3%. 94: The balanceable part of the MD step is 51%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.6%. 94: 94: 94: NOTE: 46 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.023 0.012 198.4 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 127.579 0.188 0.677 0.018 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 94: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (150 ms) 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest (150 ms total) 94: 94: [----------] Global test environment tear-down 94: [==========] 1 test from 1 test suite ran. (166 ms total) 94: [ PASSED ] 1 test. 94/103 Test #94: MdrunCoordinationBasicTests2Ranks ......... Passed 0.19 sec test 95 Start 95: MdrunCoordinationCouplingTests1Rank 95: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 95: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 95: Test timeout computed to be: 1920 95: [==========] Running 25 tests from 1 test suite. 95: [----------] Global test environment set-up. 95: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 96.714 0.248 0.893 0.013 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 142.851 0.168 0.605 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 4. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 4. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.005 0.005 98.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 318.739 0.075 0.271 0.044 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 133.297 0.180 0.648 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 128.066 0.187 0.675 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.006 0.006 98.8 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 254.602 0.094 0.339 0.035 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (133 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 111.288 0.216 0.776 0.015 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 135.813 0.177 0.636 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.008 0.008 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 185.432 0.129 0.466 0.026 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 108.238 0.222 0.798 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 98.942 0.243 0.873 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 93.800 0.256 0.921 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (150 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.020 0.020 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 73.191 0.328 1.180 0.010 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.008 0.008 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 173.739 0.138 0.497 0.024 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 123.459 0.194 0.700 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 110.695 0.217 0.781 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 104.497 0.230 0.827 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.017 0.017 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 86.156 0.279 1.003 0.012 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (159 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.017 0.018 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 83.802 0.286 1.031 0.012 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 159.493 0.150 0.542 0.022 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 138.724 0.173 0.623 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 103.941 0.231 0.831 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 99.878 0.240 0.865 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 106.448 0.225 0.812 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (154 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.023 0.023 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 64.483 0.372 1.340 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 122.777 0.195 0.704 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 132.216 0.182 0.653 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 109.578 0.219 0.788 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 100.205 0.240 0.862 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 95.056 0.252 0.909 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (165 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.019 0.019 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 78.407 0.306 1.102 0.011 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 142.313 0.169 0.607 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 145.208 0.165 0.595 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 115.508 0.208 0.748 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 113.578 0.211 0.761 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 138.855 0.173 0.622 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (151 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.019 0.019 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 78.270 0.307 1.104 0.011 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.008 0.009 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 171.868 0.140 0.503 0.024 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 153.688 0.156 0.562 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 109.417 0.219 0.790 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 114.242 0.210 0.756 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 106.082 0.226 0.814 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (153 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.021 0.021 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 68.364 0.351 1.264 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 119.686 0.201 0.722 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 125.698 0.191 0.687 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 95.433 0.251 0.905 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 91.708 0.262 0.942 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.021 0.021 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 70.496 0.340 1.226 0.010 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (174 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.023 0.023 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 63.513 0.378 1.360 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.013 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 117.175 0.205 0.737 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 117.692 0.204 0.734 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.032 0.032 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 46.434 0.517 1.861 0.006 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 95.906 0.250 0.901 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 120.186 0.200 0.719 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (521 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.018 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 83.228 0.288 1.038 0.012 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 133.505 0.180 0.647 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 141.256 0.170 0.612 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 136.125 0.176 0.635 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 155.378 0.154 0.556 0.022 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 107.283 0.224 0.805 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (149 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.029 0.029 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 50.403 0.476 1.714 0.007 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 111.054 0.216 0.778 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 116.119 0.207 0.744 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.008 0.008 98.9 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 177.503 0.135 0.487 0.025 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.012 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 127.512 0.188 0.678 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.019 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 79.296 0.303 1.090 0.011 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (171 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.019 0.020 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 75.084 0.320 1.151 0.010 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.006 0.006 98.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 248.191 0.097 0.348 0.034 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 165.951 0.145 0.521 0.023 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 120.531 0.199 0.717 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 93.806 0.256 0.921 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 119.190 0.201 0.725 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (151 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.007 0.007 99.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 210.489 0.114 0.410 0.029 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 156.020 0.154 0.554 0.022 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 4. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 4. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.022 0.022 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 67.662 0.355 1.277 0.009 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 99.236 0.242 0.871 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 126.120 0.190 0.685 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 103.574 0.232 0.834 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (155 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.019 0.019 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 75.478 0.318 1.145 0.010 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 169.294 0.142 0.510 0.024 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 167.267 0.143 0.517 0.023 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 118.969 0.202 0.726 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 126.751 0.189 0.682 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 104.178 0.230 0.829 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (151 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.021 0.021 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 68.383 0.351 1.263 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 110.870 0.216 0.779 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 154.742 0.155 0.558 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 93.692 0.256 0.922 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 95.632 0.251 0.903 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 94.287 0.255 0.916 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (168 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.022 0.022 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 67.749 0.354 1.275 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 142.369 0.169 0.607 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 135.633 0.177 0.637 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 120.491 0.199 0.717 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 124.832 0.192 0.692 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 130.386 0.184 0.663 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (156 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.020 0.021 99.8 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 71.488 0.336 1.209 0.010 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 157.903 0.152 0.547 0.022 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 4. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 4. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.007 0.008 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 195.271 0.123 0.442 0.027 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 95.925 0.250 0.901 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 94.425 0.254 0.915 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 97.848 0.245 0.883 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (160 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.019 0.019 99.8 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 79.082 0.303 1.093 0.011 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 153.723 0.156 0.562 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 116.332 0.206 0.743 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 107.691 0.223 0.802 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 103.066 0.233 0.838 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 104.525 0.230 0.827 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (157 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.020 0.020 99.8 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 72.067 0.333 1.199 0.010 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 155.677 0.154 0.555 0.022 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 159.254 0.151 0.543 0.022 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 143.396 0.167 0.603 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 100.775 0.238 0.857 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 93.293 0.257 0.926 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (155 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.025 0.025 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 58.726 0.409 1.471 0.008 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 134.443 0.179 0.643 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 149.116 0.161 0.579 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 91.016 0.264 0.949 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 94.828 0.253 0.911 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 90.544 0.265 0.954 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (169 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.023 0.023 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 64.671 0.371 1.336 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 132.586 0.181 0.652 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 128.842 0.186 0.671 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 96.195 0.249 0.898 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.017 0.017 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 88.408 0.271 0.977 0.012 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 113.950 0.211 0.758 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (166 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.018 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 80.975 0.296 1.067 0.011 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 110.162 0.218 0.784 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 123.667 0.194 0.699 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 101.501 0.236 0.851 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 97.118 0.247 0.890 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 150.755 0.159 0.573 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (160 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.022 0.022 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 65.721 0.365 1.315 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 123.647 0.194 0.699 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 107.635 0.223 0.803 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 102.477 0.234 0.843 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.020 0.020 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 74.585 0.322 1.158 0.010 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.019 0.019 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 77.289 0.311 1.118 0.011 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (177 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.030 0.030 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 49.327 0.487 1.752 0.007 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.016 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 94.682 0.253 0.913 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 4 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 148.484 0.162 0.582 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 4 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 103.073 0.233 0.838 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 4 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.024 0.024 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 61.466 0.390 1.406 0.009 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 4 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 138.577 0.173 0.623 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (181 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 90.516 0.265 0.955 0.013 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 98.9 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 168.649 0.142 0.512 0.023 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 124.328 0.193 0.695 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.014 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 108.624 0.221 0.795 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.019 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 79.386 0.302 1.088 0.011 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.018 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 79.437 0.302 1.088 0.011 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (184 ms) 95: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (4382 ms total) 95: 95: [----------] Global test environment tear-down 95: [==========] 25 tests from 1 test suite ran. (4398 ms total) 95: [ PASSED ] 25 tests. 95/103 Test #95: MdrunCoordinationCouplingTests1Rank ....... Passed 4.43 sec test 96 Start 96: MdrunCoordinationCouplingTests2Ranks 96: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 96: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 96: Test timeout computed to be: 1920 96: [==========] Running 25 tests from 1 test suite. 96: [----------] Global test environment set-up. 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.5%. 96: The balanceable part of the MD step is 56%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.046 0.023 199.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 63.151 0.380 1.368 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.4%. 96: The balanceable part of the MD step is 54%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 92.093 0.261 0.938 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.6%. 96: The balanceable part of the MD step is 47%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.021 0.011 198.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 138.981 0.173 0.622 0.019 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.7%. 96: The balanceable part of the MD step is 45%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.3%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.047 0.023 199.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 62.610 0.383 1.380 0.009 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.8%. 96: The balanceable part of the MD step is 48%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.4%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 91.800 0.261 0.941 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.2%. 96: The balanceable part of the MD step is 46%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.6%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.038 0.019 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 77.483 0.310 1.115 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (190 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.0%. 96: The balanceable part of the MD step is 57%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.6%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.058 0.029 199.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 50.115 0.479 1.724 0.007 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.5%. 96: The balanceable part of the MD step is 54%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 97.809 0.245 0.883 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.9%. 96: The balanceable part of the MD step is 50%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.4%. 96: 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.093 0.046 199.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 31.638 0.759 2.731 0.004 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.8%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.4%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.050 0.025 199.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 58.474 0.410 1.478 0.008 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.9%. 96: The balanceable part of the MD step is 47%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.4%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 100.078 0.240 0.863 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.0%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.5%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.040 0.020 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 73.874 0.325 1.170 0.010 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (231 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.3%. 96: The balanceable part of the MD step is 58%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.046 0.023 199.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 64.131 0.374 1.347 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.6%. 96: The balanceable part of the MD step is 55%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.9%. 96: 96: 96: NOTE: 43 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.009 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 156.456 0.153 0.552 0.022 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.4%. 96: The balanceable part of the MD step is 51%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 198.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 116.752 0.206 0.740 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.0%. 96: The balanceable part of the MD step is 50%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.5%. 96: 96: 96: NOTE: 44 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.009 197.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 168.742 0.142 0.512 0.023 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.8%. 96: The balanceable part of the MD step is 50%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.4%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 98.478 0.244 0.877 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.3%. 96: The balanceable part of the MD step is 50%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.2%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.056 0.028 199.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 52.032 0.461 1.661 0.007 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (181 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.7%. 96: The balanceable part of the MD step is 58%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.0%. 96: 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.119 0.060 199.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 24.621 0.975 3.509 0.003 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.4%. 96: The balanceable part of the MD step is 54%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.069 0.035 199.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 42.234 0.568 2.046 0.006 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.1%. 96: The balanceable part of the MD step is 51%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.6%. 96: 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.022 0.011 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 130.218 0.184 0.664 0.018 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.3%. 96: The balanceable part of the MD step is 50%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.2%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 91.984 0.261 0.939 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.2%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.6%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.037 0.019 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 79.120 0.303 1.092 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.6%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.3%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.043 0.022 199.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 67.694 0.355 1.276 0.009 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (242 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.042 0.021 199.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 70.261 0.342 1.230 0.010 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 112.773 0.213 0.766 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 43 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.008 197.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 194.399 0.123 0.444 0.027 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.022 0.011 197.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 133.647 0.180 0.646 0.019 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.076 0.038 199.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 38.714 0.620 2.232 0.005 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.009 196.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 166.343 0.144 0.519 0.023 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (187 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.034 0.017 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 84.850 0.283 1.018 0.012 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 40 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.007 196.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 216.237 0.111 0.400 0.030 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.008 197.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 191.623 0.125 0.451 0.027 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.022 0.011 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 130.776 0.184 0.661 0.018 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.052 0.026 199.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 56.110 0.428 1.540 0.008 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 197.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 115.967 0.207 0.745 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (170 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.064 0.032 199.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 45.723 0.525 1.890 0.006 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 197.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 122.979 0.195 0.703 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 43 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.007 196.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 218.670 0.110 0.395 0.030 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.012 197.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 123.714 0.194 0.698 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.010 197.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 151.416 0.159 0.571 0.021 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.015 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 95.395 0.252 0.906 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (171 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 99.533 0.241 0.868 0.014 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 43 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.016 0.008 196.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 176.327 0.136 0.490 0.024 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.010 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 151.017 0.159 0.572 0.021 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.022 0.011 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 133.830 0.179 0.646 0.019 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.020 0.010 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 141.763 0.169 0.609 0.020 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.040 0.020 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 72.239 0.332 1.196 0.010 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (157 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 96.518 0.249 0.895 0.013 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 44 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.008 197.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 173.555 0.138 0.498 0.024 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.020 0.010 197.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 148.627 0.161 0.581 0.021 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 88.951 0.270 0.971 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.018 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 82.603 0.291 1.046 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 197.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 112.250 0.214 0.770 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (164 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.048 0.024 199.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 61.538 0.390 1.404 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 115.707 0.207 0.747 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.021 0.011 197.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 135.261 0.177 0.639 0.019 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.036 0.018 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 80.784 0.297 1.070 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.036 0.018 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 81.071 0.296 1.066 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 198.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 97.252 0.247 0.888 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (181 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.041 0.020 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 72.041 0.333 1.199 0.010 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.014 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 104.267 0.230 0.829 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 112.677 0.213 0.767 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.036 0.018 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 80.142 0.299 1.078 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.037 0.019 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 78.564 0.305 1.100 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.017 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 84.025 0.286 1.028 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (186 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.039 0.020 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 74.706 0.321 1.157 0.010 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 119.177 0.201 0.725 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.020 0.010 198.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 145.030 0.165 0.596 0.020 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 98.297 0.244 0.879 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.034 0.017 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 85.604 0.280 1.009 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.015 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 95.016 0.253 0.909 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (179 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.040 0.020 199.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 72.351 0.332 1.194 0.010 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 198.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 95.787 0.251 0.902 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.022 0.011 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 132.737 0.181 0.651 0.018 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 90.872 0.264 0.951 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 99.837 0.240 0.865 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 113.918 0.211 0.758 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (175 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.036 0.018 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 81.939 0.293 1.054 0.011 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 114.861 0.209 0.752 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.013 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 109.456 0.219 0.789 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.014 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 104.093 0.231 0.830 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 88.348 0.272 0.978 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.017 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 84.547 0.284 1.022 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (174 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.047 0.024 199.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 62.163 0.386 1.390 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 120.216 0.200 0.719 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.011 198.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 127.887 0.188 0.676 0.018 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 88.460 0.271 0.977 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 89.862 0.267 0.961 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.036 0.018 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 82.242 0.292 1.051 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (180 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.048 0.024 199.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 60.660 0.396 1.424 0.008 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 198.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 120.745 0.199 0.716 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 112.782 0.213 0.766 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.036 0.018 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 81.426 0.295 1.061 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.034 0.017 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 86.300 0.278 1.001 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 92.392 0.260 0.935 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (183 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.9%. 96: The balanceable part of the MD step is 61%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.5%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.038 0.019 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 77.220 0.311 1.119 0.011 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.1%. 96: The balanceable part of the MD step is 62%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.013 197.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 109.118 0.220 0.792 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.2%. 96: The balanceable part of the MD step is 55%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 197.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 109.845 0.218 0.787 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.6%. 96: The balanceable part of the MD step is 53%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.3%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.037 0.019 198.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 78.746 0.305 1.097 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.0%. 96: The balanceable part of the MD step is 53%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.5%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 96.937 0.248 0.891 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.6%. 96: The balanceable part of the MD step is 53%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.3%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.036 0.018 198.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 80.024 0.300 1.080 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (177 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.8%. 96: The balanceable part of the MD step is 61%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.5%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.053 0.027 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 55.093 0.436 1.568 0.008 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.9%. 96: The balanceable part of the MD step is 61%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.2%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 197.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 117.437 0.204 0.736 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.7%. 96: The balanceable part of the MD step is 59%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.4%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 197.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 118.667 0.202 0.728 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.1%. 96: The balanceable part of the MD step is 58%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.016 197.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 92.101 0.261 0.938 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.0%. 96: The balanceable part of the MD step is 58%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.5%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.016 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 93.524 0.257 0.924 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.5%. 96: The balanceable part of the MD step is 58%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.3%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 98.716 0.243 0.875 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (177 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.2%. 96: The balanceable part of the MD step is 60%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.3%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.045 0.023 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 64.571 0.372 1.338 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.8%. 96: The balanceable part of the MD step is 62%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.5%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.012 197.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 117.743 0.204 0.734 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.9%. 96: The balanceable part of the MD step is 59%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.6%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 197.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 89.531 0.268 0.965 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.9%. 96: The balanceable part of the MD step is 58%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.5%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.018 197.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 82.948 0.289 1.042 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.8%. 96: The balanceable part of the MD step is 58%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.4%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 197.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 87.379 0.275 0.989 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.7%. 96: The balanceable part of the MD step is 58%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.0%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 88.418 0.271 0.977 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (182 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.048 0.024 198.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 61.061 0.393 1.415 0.008 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 196.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 111.260 0.216 0.777 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 196.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 119.716 0.200 0.722 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.018 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 83.666 0.287 1.033 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.016 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 89.075 0.269 0.970 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.034 0.017 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 86.003 0.279 1.005 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (183 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.046 0.023 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 63.379 0.379 1.363 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 196.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 121.023 0.198 0.714 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 196.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 109.768 0.219 0.787 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.040 0.020 197.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 72.542 0.331 1.191 0.010 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.034 0.017 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 84.303 0.285 1.025 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.043 0.022 198.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 67.449 0.356 1.281 0.009 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (190 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 90.440 0.265 0.955 0.013 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 196.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 118.061 0.203 0.732 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.012 196.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 125.701 0.191 0.687 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.038 0.019 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 76.420 0.314 1.131 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.037 0.019 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 79.187 0.303 1.091 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.040 0.020 198.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 72.581 0.331 1.190 0.010 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (180 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.052 0.026 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 55.696 0.431 1.551 0.008 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.014 0.007 193.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 210.428 0.114 0.411 0.029 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 196.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 117.102 0.205 0.738 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.040 0.020 198.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 72.503 0.331 1.192 0.010 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.039 0.020 197.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 73.846 0.325 1.170 0.010 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.014 197.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 104.686 0.229 0.825 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (180 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.058 0.029 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 50.044 0.480 1.726 0.007 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 196.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 120.305 0.199 0.718 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 196.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 109.849 0.218 0.787 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 196.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 117.443 0.204 0.736 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.018 197.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 83.322 0.288 1.037 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.018 197.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 82.168 0.292 1.052 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (184 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.036 0.018 197.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 80.248 0.299 1.077 0.011 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.013 196.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 108.950 0.220 0.793 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 196.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 118.356 0.203 0.730 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 197.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 87.887 0.273 0.983 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.016 197.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 92.912 0.258 0.930 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.034 0.017 197.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 85.757 0.280 1.008 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (174 ms) 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (4593 ms total) 96: 96: [----------] Global test environment tear-down 96: [==========] 25 tests from 1 test suite ran. (4609 ms total) 96: [ PASSED ] 25 tests. 96/103 Test #96: MdrunCoordinationCouplingTests2Ranks ...... Passed 4.64 sec test 97 Start 97: MdrunCoordinationConstraintsTests1Rank 97: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 97: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 97: Test timeout computed to be: 1920 97: [==========] Running 13 tests from 1 test suite. 97: [----------] Global test environment set-up. 97: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.047 0.047 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 31.246 0.768 2.765 0.005 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.141 0.683 2.459 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.046 0.046 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 31.972 0.751 2.702 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.047 0.048 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 30.914 0.776 2.795 0.005 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.049 0.049 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 29.778 0.806 2.901 0.005 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.048 0.048 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 30.632 0.783 2.821 0.005 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (5051 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.523 0.716 2.577 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.694 0.692 2.490 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.041 0.041 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.610 0.674 2.426 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.829 0.709 2.554 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.867 0.709 2.551 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.175 0.702 2.528 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (5051 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.273 0.721 2.597 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.041 0.041 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.419 0.678 2.439 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.315 0.680 2.447 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.385 0.698 2.513 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.393 0.698 2.512 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.279 0.700 2.520 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (5031 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.163 0.724 2.605 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.041 0.041 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.408 0.678 2.440 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.081 0.684 2.463 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.384 0.698 2.513 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.951 0.707 2.545 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.077 0.704 2.535 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (5027 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.251 0.722 2.598 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.554 0.695 2.500 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.006 0.686 2.468 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.862 0.709 2.552 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.023 0.023 99.6 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 63.291 0.379 1.365 0.011 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.558 0.715 2.575 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (5054 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.017 0.727 2.617 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.851 0.689 2.479 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.047 0.047 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 30.982 0.775 2.789 0.005 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.049 0.049 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 30.142 0.796 2.866 0.005 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.028 0.028 99.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 51.673 0.464 1.672 0.009 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.844 0.709 2.553 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (5051 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.096 0.725 2.611 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.675 0.692 2.492 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.910 0.687 2.475 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.283 0.700 2.520 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.031 0.705 2.539 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.715 0.712 2.563 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (5043 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.238 0.722 2.599 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.836 0.689 2.480 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.846 0.689 2.479 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.827 0.709 2.554 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.759 0.711 2.559 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.752 0.711 2.560 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (5035 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.293 0.721 2.595 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.875 0.688 2.477 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.887 0.688 2.477 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.808 0.710 2.556 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.822 0.710 2.555 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.354 0.720 2.590 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (5043 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.784 0.732 2.635 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.262 0.700 2.522 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.373 0.698 2.514 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.498 0.716 2.579 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.617 0.714 2.570 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.598 0.714 2.572 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (5053 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.761 0.733 2.637 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.071 0.704 2.536 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.084 0.704 2.535 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.150 0.724 2.606 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.704 0.712 2.563 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.150 0.724 2.606 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (5047 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.304 0.721 2.594 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.418 0.697 2.510 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.553 0.695 2.500 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.040 0.726 2.615 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.026 0.727 2.616 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.427 0.718 2.585 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (5050 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.807 0.732 2.634 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.727 0.691 2.488 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.133 0.703 2.531 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.272 0.721 2.597 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.657 0.713 2.567 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.077 0.726 2.612 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (5045 ms) 97: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (65589 ms total) 97: 97: [----------] Global test environment tear-down 97: [==========] 13 tests from 1 test suite ran. (65605 ms total) 97: [ PASSED ] 13 tests. 97/103 Test #97: MdrunCoordinationConstraintsTests1Rank .... Passed 65.64 sec test 98 Start 98: MdrunCoordinationConstraintsTests2Ranks 98: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 98: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 98: Test timeout computed to be: 1920 98: [==========] Running 13 tests from 1 test suite. 98: [----------] Global test environment set-up. 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 2.5%. 98: The balanceable part of the MD step is 36%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 0.9%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.095 0.048 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 30.791 0.779 2.806 0.005 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 4.9%. 98: The balanceable part of the MD step is 50%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.4%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.757 0.711 2.560 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 3.7%. 98: The balanceable part of the MD step is 46%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.7%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.084 0.042 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.692 0.692 2.490 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 4.7%. 98: The balanceable part of the MD step is 45%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.1%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.245 0.722 2.599 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 4.1%. 98: The balanceable part of the MD step is 45%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.8%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.626 0.714 2.569 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 4.6%. 98: The balanceable part of the MD step is 43%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.0%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.424 0.718 2.585 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (5229 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 2.5%. 98: The balanceable part of the MD step is 58%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.4%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.048 0.726 2.614 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 3.7%. 98: The balanceable part of the MD step is 54%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.0%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.084 0.042 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.699 0.692 2.490 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 4.2%. 98: The balanceable part of the MD step is 49%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.1%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.305 0.700 2.519 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 4.2%. 98: The balanceable part of the MD step is 48%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.0%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.470 0.717 2.581 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 4.0%. 98: The balanceable part of the MD step is 48%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.9%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.207 0.723 2.602 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 4.1%. 98: The balanceable part of the MD step is 35%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.4%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.380 0.719 2.588 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (5212 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 2.2%. 98: The balanceable part of the MD step is 56%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.2%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.800 0.732 2.634 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 3.4%. 98: The balanceable part of the MD step is 54%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.8%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.423 0.697 2.510 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.3%. 98: The balanceable part of the MD step is 45%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.4%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.430 0.697 2.509 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 4.1%. 98: The balanceable part of the MD step is 48%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.0%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.697 0.734 2.642 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 3.6%. 98: The balanceable part of the MD step is 48%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.7%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.045 195.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.690 0.734 2.643 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 3.7%. 98: The balanceable part of the MD step is 48%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.7%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.092 0.046 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.922 0.752 2.707 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (5236 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.529 0.738 2.656 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.168 0.702 2.529 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.084 0.042 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.723 0.691 2.488 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.637 0.735 2.647 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.319 0.699 2.518 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.013 0.727 2.617 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (5222 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.624 0.736 2.648 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.529 0.716 2.577 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.837 0.731 2.631 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.422 0.697 2.510 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.987 0.706 2.542 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.725 0.712 2.562 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (5219 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.176 0.723 2.604 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.084 0.042 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.983 0.686 2.470 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.084 0.042 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.697 0.692 2.490 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.647 0.713 2.568 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.157 0.078 199.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 18.729 1.281 4.613 0.003 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.578 0.715 2.573 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (5250 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.076 0.038 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 38.653 0.621 2.235 0.007 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.474 0.717 2.581 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.557 0.695 2.500 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.905 0.708 2.548 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.486 0.739 2.660 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.920 0.729 2.625 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (5227 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.703 0.734 2.642 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.416 0.697 2.510 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.042 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.597 0.694 2.497 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.911 0.729 2.625 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.871 0.730 2.628 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.459 0.717 2.582 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (5213 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.505 0.738 2.658 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.993 0.706 2.542 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.780 0.710 2.558 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.092 0.046 199.6 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.692 0.757 2.726 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.773 0.732 2.636 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.054 0.027 199.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 54.362 0.441 1.589 0.009 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (5207 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 2.3%. 98: The balanceable part of the MD step is 62%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.4%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.093 0.047 199.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.495 0.762 2.743 0.005 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 3.9%. 98: The balanceable part of the MD step is 62%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.4%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.554 0.715 2.575 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.0%. 98: The balanceable part of the MD step is 55%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.7%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.440 0.740 2.663 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 4.5%. 98: The balanceable part of the MD step is 52%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.3%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.918 0.729 2.625 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 4.6%. 98: The balanceable part of the MD step is 52%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.4%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.907 0.729 2.626 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 4.5%. 98: The balanceable part of the MD step is 52%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.4%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.486 0.717 2.580 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (5212 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 1.0%. 98: The balanceable part of the MD step is 37%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 0.4%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.097 0.049 199.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 30.263 0.793 2.855 0.005 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 2.8%. 98: The balanceable part of the MD step is 61%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.7%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.252 0.701 2.522 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 3.9%. 98: The balanceable part of the MD step is 58%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.3%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 198.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.565 0.715 2.574 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 3.4%. 98: The balanceable part of the MD step is 57%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.9%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.886 0.730 2.627 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 27.7%. 98: The balanceable part of the MD step is 42%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 11.8%. 98: 98: NOTE: 11.8 % of the available CPU time was lost due to load imbalance 98: in the domain decomposition. 98: You can consider manually changing the decomposition (option -dd); 98: e.g. by using fewer domains along the box dimension in which there is 98: considerable inhomogeneity in the simulated system. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.047 193.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.560 0.760 2.738 0.005 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB was off during the run due to low measured imbalance. 98: Average load imbalance: 3.2%. 98: The balanceable part of the MD step is 56%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 1.8%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.786 0.732 2.635 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (5232 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.455 0.739 2.662 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 198.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.557 0.715 2.575 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 198.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.438 0.718 2.584 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 198.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.769 0.732 2.637 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 198.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.933 0.729 2.624 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.814 0.731 2.633 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (5201 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.092 0.046 198.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.758 0.756 2.721 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 198.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.162 0.724 2.605 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 198.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.772 0.711 2.558 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.091 0.046 198.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.994 0.750 2.701 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.094 0.047 198.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.008 0.774 2.786 0.005 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 198.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.457 0.739 2.662 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (5273 ms) 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (67940 ms total) 98: 98: [----------] Global test environment tear-down 98: [==========] 13 tests from 1 test suite ran. (67956 ms total) 98: [ PASSED ] 13 tests. 98/103 Test #98: MdrunCoordinationConstraintsTests2Ranks ... Passed 67.98 sec test 99 Start 99: MdrunFEPTests 99: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunFEPTests.xml" 99: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 99: Test timeout computed to be: 600 99: [==========] Running 14 tests from 2 test suites. 99: [----------] Global test environment set-up. 99: [----------] 2 tests from ExpandedEnsembleTest 99: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 79.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There was 1 NOTE 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun '30 atom system in water' 99: 16 steps, 0.0 ps. 99: Generated 2485 of the 2485 non-bonded parameter combinations 99: 99: Generated 2485 of the 2485 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'nonanol' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.032 0.016 198.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 92.517 0.259 0.934 0.039 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 99: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 99: 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun '30 atom system in water' 99: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.047 0.024 198.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 32.526 0.738 2.656 0.014 99: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (114 ms) 99: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 79.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There was 1 NOTE 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun '30 atom system in water' 99: 1 steps, 0.0 ps. 99: Generated 2485 of the 2485 non-bonded parameter combinations 99: 99: Generated 2485 of the 2485 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'nonanol' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: NOTE: 14 % of the run time was spent in pair search, 99: you might want to increase nstlist (this has no effect on accuracy) 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.081 0.041 199.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 4.252 5.645 20.321 0.002 99: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (85 ms) 99: [----------] 2 tests from ExpandedEnsembleTest (200 ms total) 99: 99: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 3 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to 1596453876 99: 99: Generated 153 of the 153 non-bonded parameter combinations 99: 99: Generated 153 of the 153 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'ASN' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.238 0.119 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 15.209 1.578 5.681 0.031 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (362 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 3 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to -1107575041 99: 99: Generated 153 of the 153 non-bonded parameter combinations 99: 99: Generated 153 of the 153 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'ASN' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.236 0.118 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 15.329 1.566 5.636 0.031 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (356 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 99: With PME there is a minor soft core effect present at the cut-off, 99: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 99: energy conservation, but usually other effects dominate. With a common 99: sigma value of 0.34 nm the fraction of the particle-particle potential at 99: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 4 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to 1861744892 99: 99: Generated 153 of the 153 non-bonded parameter combinations 99: 99: Generated 153 of the 153 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'ASN' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.192 0.096 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 18.914 1.269 4.568 0.039 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (327 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 99: With PME there is a minor soft core effect present at the cut-off, 99: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 99: energy conservation, but usually other effects dominate. With a common 99: sigma value of 0.34 nm the fraction of the particle-particle potential at 99: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: 99: NOTE 3 [file topol.top, line 155]: 99: System has non-zero total charge: 1.000000 99: Total charge should normally be an integer. See 99: https://manual.gromacs.org/current/user-guide/floating-point.html 99: for discussion on how close it should be to an integer. 99: 99: 99: 99: 99: WARNING 2 [file topol.top, line 155]: 99: You are using Ewald electrostatics in a system with net charge. This can 99: lead to severe artifacts, such as ions moving into regions with low 99: dielectric, due to the uniform background charge. We suggest to 99: neutralize your system with counter ions, possibly in combination with a 99: physiological salt concentration. 99: 99: Setting the LD random seed to -171442181 99: 99: Generated 171 of the 171 non-bonded parameter combinations 99: 99: Generated 171 of the 171 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Excluding 1 bonded neighbours molecule type 'NA' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'ASN' 99: 99: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 99: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 99: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 99: Charge 99: J. Chem. Theory Comput. (2014) 99: https://doi.org/10.1021/ct400626b 99: -------- -------- --- Thank You --- -------- -------- 99: 99: Number of degrees of freedom in T-Coupling group System is 358.00 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 5 NOTEs 99: 99: There were 2 WARNINGs 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: There are: 1 Ion residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 99: 99: Estimate for the relative computational load of the PME mesh part: 0.92 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.141 0.070 199.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 25.761 0.932 3.354 0.053 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (120 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 99: With PME there is a minor soft core effect present at the cut-off, 99: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 99: energy conservation, but usually other effects dominate. With a common 99: sigma value of 0.34 nm the fraction of the particle-particle potential at 99: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: 99: NOTE 3 [file topol.top, line 165]: 99: System has non-zero total charge: 1.000000 99: Total charge should normally be an integer. See 99: https://manual.gromacs.org/current/user-guide/floating-point.html 99: for discussion on how close it should be to an integer. 99: 99: 99: 99: 99: WARNING 2 [file topol.top, line 165]: 99: You are using Ewald electrostatics in a system with net charge. This can 99: lead to severe artifacts, such as ions moving into regions with low 99: dielectric, due to the uniform background charge. We suggest to 99: neutralize your system with counter ions, possibly in combination with a 99: physiological salt concentration. 99: 99: Setting the LD random seed to -68747265 99: 99: Generated 190 of the 190 non-bonded parameter combinations 99: 99: Generated 190 of the 190 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Excluding 1 bonded neighbours molecule type 'NA' 99: 99: turning H bonds into constraints... 99: 99: Excluding 1 bonded neighbours molecule type 'CL' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'CL' 99: 99: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 99: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 99: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 99: Charge 99: J. Chem. Theory Comput. (2014) 99: https://doi.org/10.1021/ct400626b 99: -------- -------- --- Thank You --- -------- -------- 99: 99: Number of degrees of freedom in T-Coupling group System is 361.00 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 5 NOTEs 99: 99: There were 2 WARNINGs 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: There are: 2 Ion residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 99: 99: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 99: 99: Estimate for the relative computational load of the PME mesh part: 0.92 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.157 0.078 199.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 23.150 1.037 3.732 0.048 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (122 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 99: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 99: and vdw_modifier=Force-switch 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 4 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 100 steps, 0.1 ps. 99: Setting the LD random seed to -571081233 99: 99: Generated 153 of the 153 non-bonded parameter combinations 99: 99: Generated 153 of the 153 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'ASN' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.834 0.417 200.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 20.922 1.147 4.130 0.043 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (664 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: 99: WARNING 2 [file topol.top, line 72]: 99: No default Bond types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '7 8 1'. 99: 99: 99: WARNING 3 [file topol.top, line 73]: 99: No default Bond types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '7 9 1'. 99: 99: 99: WARNING 4 [file topol.top, line 98]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '6 5 7 1'. 99: 99: 99: WARNING 5 [file topol.top, line 99]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '5 7 8 1'. 99: 99: 99: WARNING 6 [file topol.top, line 100]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '5 7 9 1'. 99: 99: 99: WARNING 7 [file topol.top, line 101]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '8 7 9 1'. 99: 99: 99: WARNING 8 [file topol.top, line 111]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '1 5 7 8 3'. 99: 99: 99: WARNING 9 [file topol.top, line 112]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '1 5 7 9 3'. 99: 99: 99: WARNING 10 [file topol.top, line 113]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '6 5 7 8 3'. 99: 99: 99: WARNING 11 [file topol.top, line 114]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '6 5 7 9 3'. 99: 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 2 NOTEs 99: 99: There were 11 WARNINGs 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to -152053313 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.352 0.176 199.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 10.302 2.330 8.386 0.021 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (408 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: 99: WARNING 2 [file topol.top, line 72]: 99: No default Bond types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '7 8 1'. 99: 99: 99: WARNING 3 [file topol.top, line 73]: 99: No default Bond types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '7 9 1'. 99: 99: 99: WARNING 4 [file topol.top, line 98]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '6 5 7 1'. 99: 99: 99: WARNING 5 [file topol.top, line 99]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '5 7 8 1'. 99: 99: 99: WARNING 6 [file topol.top, line 100]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '5 7 9 1'. 99: 99: 99: WARNING 7 [file topol.top, line 101]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '8 7 9 1'. 99: 99: 99: WARNING 8 [file topol.top, line 111]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '1 5 7 8 3'. 99: 99: 99: WARNING 9 [file topol.top, line 112]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '1 5 7 9 3'. 99: 99: 99: WARNING 10 [file topol.top, line 113]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '6 5 7 8 3'. 99: 99: 99: WARNING 11 [file topol.top, line 114]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '6 5 7 9 3'. 99: 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 99: Removing center of mass motion in the presence of position restraints 99: might cause artifacts. When you are using position restraints to 99: equilibrate a macro-molecule, the artifacts are usually negligible. 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 3 NOTEs 99: 99: There were 11 WARNINGs 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to -622889025 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.338 0.169 199.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 10.713 2.240 8.065 0.022 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (402 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 2 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to -80257089 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.81 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.149 0.075 199.6 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 24.310 0.987 3.554 0.050 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (301 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: There was 1 NOTE 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.063 0.032 199.2 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 56.972 0.421 1.517 0.117 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to 1875899483 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.81 99: 99: This run will generate roughly 0 Mb of data 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (294 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 99: With PME there is a minor soft core effect present at the cut-off, 99: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 99: energy conservation, but usually other effects dominate. With a common 99: sigma value of 0.34 nm the fraction of the particle-particle potential at 99: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 3 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to 2013457407 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.234 0.117 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 15.481 1.550 5.581 0.032 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (346 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 99: With PME there is a minor soft core effect present at the cut-off, 99: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 99: energy conservation, but usually other effects dominate. With a common 99: sigma value of 0.34 nm the fraction of the particle-particle potential at 99: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 3 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to -144482305 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.81 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.157 0.079 199.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 23.065 1.041 3.746 0.047 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (311 ms) 99: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (4021 ms total) 99: 99: [----------] Global test environment tear-down 99: [==========] 14 tests from 2 test suites ran. (4253 ms total) 99: [ PASSED ] 14 tests. 99/103 Test #99: MdrunFEPTests ............................. Passed 4.28 sec test 100 Start 100: MdrunPullTests 100: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunPullTests.xml" 100: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 100: Test timeout computed to be: 600 100: [==========] Running 4 tests from 1 test suite. 100: [----------] Global test environment set-up. 100: [----------] 4 tests from PullTest/PullIntegrationTest 100: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 100: Generating 1-4 interactions: fudge = 0.5 100: Pull group 1 'r_1' has 3 atoms 100: Pull group 2 'r_2' has 3 atoms 100: Number of degrees of freedom in T-Coupling group System is 1293.00 100: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 100: NVE simulation: will use the initial temperature of 303.122 K for 100: determining the Verlet buffer size 100: 100: Pull group natoms pbc atom distance at start reference at t=0 100: 1 3 2 100: 2 3 5 0.575 nm 0.600 nm 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 100: Can not increase nstlist because an NVE ensemble is used 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'spc2' 100: 20 steps, 0.0 ps. 100: Generated 330891 of the 330891 non-bonded parameter combinations 100: 100: Generated 330891 of the 330891 1-4 parameter combinations 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.207 0.104 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 17.509 1.371 4.935 0.131 100: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (933 ms) 100: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 100: Generating 1-4 interactions: fudge = 0.5 100: Pull group 1 'r_1' has 3 atoms 100: Pull group 2 'r_2' has 3 atoms 100: Number of degrees of freedom in T-Coupling group System is 1293.00 100: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 100: NVE simulation: will use the initial temperature of 303.122 K for 100: determining the Verlet buffer size 100: 100: Pull group natoms pbc atom distance at start reference at t=0 100: 1 3 2 100: 2 3 5 0.301 nm 0.400 nm 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 100: Can not increase nstlist because an NVE ensemble is used 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'spc2' 100: 20 steps, 0.0 ps. 100: Generated 330891 of the 330891 non-bonded parameter combinations 100: 100: Generated 330891 of the 330891 1-4 parameter combinations 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.205 0.102 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 17.719 1.354 4.876 0.133 100: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (911 ms) 100: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 100: Generating 1-4 interactions: fudge = 0.5 100: Pull group 1 'r_1' has 3 atoms 100: Pull group 2 'r_2' has 3 atoms 100: Pull group 3 'r_3' has 3 atoms 100: Number of degrees of freedom in T-Coupling group System is 1292.00 100: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 100: NVE simulation: will use the initial temperature of 303.357 K for 100: determining the Verlet buffer size 100: 100: Pull group natoms pbc atom distance at start reference at t=0 100: 1 3 2 100: 2 3 5 0.575 nm 0.500 nm 100: 1 3 2 100: 3 3 8 0.331 nm 0.400 nm 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 100: Can not increase nstlist because an NVE ensemble is used 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'spc2' 100: 20 steps, 0.0 ps. 100: Generated 330891 of the 330891 non-bonded parameter combinations 100: 100: Generated 330891 of the 330891 1-4 parameter combinations 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.206 0.103 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 17.600 1.364 4.909 0.132 100: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (917 ms) 100: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 100: Generating 1-4 interactions: fudge = 0.5 100: Pull group 1 'r_1' has 3 atoms 100: Pull group 2 'r_2' has 3 atoms 100: Number of degrees of freedom in T-Coupling group System is 1293.00 100: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 100: NVE simulation: will use the initial temperature of 303.122 K for 100: determining the Verlet buffer size 100: 100: Pull group natoms pbc atom distance at start reference at t=0 100: 1 3 2 100: 2 3 5 0.575 nm 0.000 nm 100: 0.050 nm 0.000 nm 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 100: Can not increase nstlist because an NVE ensemble is used 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'spc2' 100: 20 steps, 0.0 ps. 100: Generated 330891 of the 330891 non-bonded parameter combinations 100: 100: Generated 330891 of the 330891 1-4 parameter combinations 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.206 0.103 199.7 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 17.595 1.364 4.911 0.132 100: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (927 ms) 100: [----------] 4 tests from PullTest/PullIntegrationTest (3690 ms total) 100: 100: [----------] Global test environment tear-down 100: [==========] 4 tests from 1 test suite ran. (3706 ms total) 100: [ PASSED ] 4 tests. 100/103 Test #100: MdrunPullTests ............................ Passed 3.74 sec test 101 Start 101: MdrunRotationTests 101: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunRotationTests.xml" 101: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 101: Test timeout computed to be: 600 101: [==========] Running 12 tests from 1 test suite. 101: [----------] Global test environment set-up. 101: [----------] 12 tests from RotationWorks/RotationTest 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 101: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: trr version: GMX_trn_file (single precision) 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -286427201 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.020 0.010 198.0 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 442.767 0.054 0.390 0.010 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (30 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 101: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -1073788977 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.016 0.008 197.9 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 556.861 0.043 0.310 0.013 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (25 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 101: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -541073537 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.038 0.019 199.1 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 233.926 0.103 0.739 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (36 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 101: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -939532801 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.038 0.019 199.1 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 236.575 0.101 0.730 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (36 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 101: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to 2140929915 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.039 0.020 199.1 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 230.175 0.104 0.751 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (36 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 101: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to 1777323519 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.039 0.020 199.1 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 228.944 0.105 0.755 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (36 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 101: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -344068 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.038 0.019 199.2 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 236.225 0.102 0.732 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (36 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 101: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -2021802053 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.038 0.019 199.2 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 234.891 0.102 0.736 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (36 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 101: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -16908301 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.045 0.023 199.2 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 199.139 0.121 0.868 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (41 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 101: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -549586961 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.050 0.025 199.3 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 180.330 0.133 0.958 0.004 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (41 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 101: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -334074894 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.056 0.028 199.4 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 159.308 0.151 1.085 0.004 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (46 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 101: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -118638673 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.051 0.026 199.3 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 174.829 0.137 0.988 0.004 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (43 ms) 101: [----------] 12 tests from RotationWorks/RotationTest (450 ms total) 101: 101: [----------] Global test environment tear-down 101: [==========] 12 tests from 1 test suite ran. (466 ms total) 101: [ PASSED ] 12 tests. 101/103 Test #101: MdrunRotationTests ........................ Passed 0.49 sec test 102 Start 102: MdrunSimulatorComparison 102: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" 102: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 102: Test timeout computed to be: 600 102: [==========] Running 0 tests from 0 test suites. 102: [==========] 0 tests from 0 test suites ran. (0 ms total) 102: [ PASSED ] 0 tests. 102: 102: YOU HAVE 82 DISABLED TESTS 102: 102/103 Test #102: MdrunSimulatorComparison .................. Passed 0.03 sec test 103 Start 103: MdrunVirtualSiteTests 103: Test command: /build/reproducible-path/gromacs-2026.2/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" 103: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests 103: Test timeout computed to be: 600 103: [==========] Running 37 tests from 2 test suites. 103: [----------] Global test environment set-up. 103: [----------] 1 test from VirtualSiteVelocityTest 103: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 103: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 103: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 103: 103: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 103: NVE simulation with an initial temperature of zero: will use a Verlet 103: buffer of 10%. Check your energy drift! 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: 103: Dynamic load balancing report: 103: DLB was off during the run due to low measured imbalance. 103: Average load imbalance: 6.2%. 103: The balanceable part of the MD step is 43%, load imbalance is computed from this. 103: Part of the total run time spent waiting due to load imbalance: 2.7%. 103: 103: 103: NOTE: 48 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.048 0.024 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 32.090 0.748 2.692 0.009 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: trr version: GMX_trn_file (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (44 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 103: NVE simulation with an initial temperature of zero: will use a Verlet 103: buffer of 10%. Check your energy drift! 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: 103: Dynamic load balancing report: 103: DLB was off during the run due to low measured imbalance. 103: Average load imbalance: 6.6%. 103: The balanceable part of the MD step is 41%, load imbalance is computed from this. 103: Part of the total run time spent waiting due to load imbalance: 2.7%. 103: 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.040 0.020 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 38.708 0.620 2.232 0.011 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (36 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 103: NVE simulation with an initial temperature of zero: will use a Verlet 103: buffer of 10%. Check your energy drift! 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: 103: Dynamic load balancing report: 103: DLB was off during the run due to low measured imbalance. 103: Average load imbalance: 6.7%. 103: The balanceable part of the MD step is 45%, load imbalance is computed from this. 103: Part of the total run time spent waiting due to load imbalance: 3.0%. 103: 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.035 0.017 198.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 44.442 0.540 1.944 0.012 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (35 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.026 0.013 198.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 59.376 0.404 1.455 0.016 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (38 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 48 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.043 0.022 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 35.818 0.670 2.412 0.010 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (47 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.039 0.020 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 39.812 0.603 2.170 0.011 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (44 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 4 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.038 0.019 198.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 40.810 0.588 2.117 0.011 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (43 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 4 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 48 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.054 0.027 199.1 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 28.580 0.840 3.023 0.008 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (51 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 4 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 48 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.043 0.021 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 36.358 0.660 2.376 0.010 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (45 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 103: NVE simulation with an initial temperature of zero: will use a Verlet 103: buffer of 10%. Check your energy drift! 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: 103: Dynamic load balancing report: 103: DLB was off during the run due to low measured imbalance. 103: Average load imbalance: 5.9%. 103: The balanceable part of the MD step is 44%, load imbalance is computed from this. 103: Part of the total run time spent waiting due to load imbalance: 2.6%. 103: 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.030 0.015 198.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 51.855 0.463 1.666 0.014 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (30 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 103: NVE simulation with an initial temperature of zero: will use a Verlet 103: buffer of 10%. Check your energy drift! 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: 103: Dynamic load balancing report: 103: DLB was off during the run due to low measured imbalance. 103: Average load imbalance: 4.7%. 103: The balanceable part of the MD step is 45%, load imbalance is computed from this. 103: Part of the total run time spent waiting due to load imbalance: 2.1%. 103: 103: 103: NOTE: 45 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.027 0.014 198.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 57.372 0.418 1.506 0.016 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (29 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.026 0.013 198.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 58.201 0.412 1.485 0.016 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (37 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.026 0.013 198.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 58.291 0.412 1.482 0.016 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (37 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.030 0.015 198.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 51.522 0.466 1.677 0.014 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (39 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.033 0.017 198.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 46.429 0.517 1.861 0.013 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (41 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.026 0.013 198.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 59.428 0.404 1.454 0.017 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (37 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.026 0.013 198.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 58.645 0.409 1.473 0.016 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (37 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.038 0.019 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 40.894 0.587 2.113 0.011 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (43 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.037 0.019 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 41.732 0.575 2.070 0.012 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (50 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.026 0.013 198.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 58.282 0.412 1.482 0.016 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (44 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.039 0.019 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 40.121 0.598 2.154 0.011 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.2-Debian_2026.2_2 (single precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (51 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 103: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (872 ms total) 103: 103: [----------] Global test environment tear-down 103: [==========] 37 tests from 2 test suites ran. (888 ms total) 103: [ PASSED ] 37 tests. 103/103 Test #103: MdrunVirtualSiteTests ..................... Passed 0.92 sec The following tests passed: GmxapiExternalInterfaceTests GmxapiInternalInterfaceTests NbLibListedForcesTests NbLibSamplesTestArgon NbLibSamplesTestMethaneWater NbLibUtilTests NbLibSetupTests NbLibTprTests NbLibIntegrationTests NbLibIntegratorTests threadMPI-mpithreads threadMPI-sync_cyclecount threadMPI-mpi_speedtest threadMPI-notmpi threadMPI-alloc_check TestUtilsUnitTests TestUtilsMpiUnitTests UtilityUnitTests MpiCommTests UtilityMpiUnitTests AwhTest DensityFittingAppliedForcesUnitTest QMMMAppliedForcesUnitTest ColvarsAppliedForcesUnitTest PlumedAppliedForcesUnitTests PlumedMDTests NNPotAppliedForcesUnitTest AppliedForcesUnitTest ListedForcesTest NbnxmTests NbnxmGpuTests GmxlibTests GmxlibGpuTests CommandLineUnitTests DomDecTests DomDecMpiTests EwaldUnitTests FFTUnitTests FmmInterfaceUnitTests GpuUtilsUnitTests GpuUtilsMpiTests HardwareUnitTests MathUnitTests MdrunUtilityUnitTests MdrunUtilityMpiUnitTests MDSpanTests MdtypesUnitTest OnlineHelpUnitTests OptionsUnitTests PbcutilUnitTest RandomUnitTests RestraintTests SerializationUnitTests TableUnitTests TaskAssignmentUnitTests GmxTimingTests TopologyTest PullTest SimdUnitTests CompatibilityHelpersTests GmxAnaTest GmxPreprocessTests Pdb2gmx1Test Pdb2gmx2Test Pdb2gmx3Test CorrelationsTest AnalysisDataUnitTests CoordinateIOTests TrajectoryAnalysisUnitTests EnergyAnalysisUnitTests ToolUnitTests ToolWithLeaksUnitTests H5mdTests FileIOTests SelectionUnitTests MdrunOutputTests MdrunModulesTests MdrunIOTests MdrunTestsOneRank MdrunTestsTwoRanks MdrunSingleRankAlgorithmsTests Minimize1RankTests Minimize2RankTests MdrunNonIntegratorTests MdrunTpiTests MdrunMpiTests MdrunMultiSimTests MdrunMultiSimReplexTests MdrunMultiSimReplexEquivalenceTests MdrunMpi1RankPmeTests MdrunMpi2RankPmeTests MdrunMpi4RankPmeTests MdrunCoordinationBasicTests1Rank MdrunCoordinationBasicTests2Ranks MdrunCoordinationCouplingTests1Rank MdrunCoordinationCouplingTests2Ranks MdrunCoordinationConstraintsTests1Rank MdrunCoordinationConstraintsTests2Ranks MdrunFEPTests MdrunPullTests MdrunRotationTests MdrunSimulatorComparison MdrunVirtualSiteTests 100% tests passed, 0 tests failed out of 103 Label Time Summary: GTest = 812.02 sec*proc (96 tests) IntegrationTest = 537.41 sec*proc (30 tests) MpiTest = 674.09 sec*proc (24 tests) QuickGpuTest = 149.76 sec*proc (24 tests) SlowGpuTest = 593.44 sec*proc (15 tests) SlowTest = 265.92 sec*proc (14 tests) UnitTest = 8.69 sec*proc (52 tests) Total Test time (real) = 383.00 sec /usr/bin/make -j4 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.2 -B/build/reproducible-path/gromacs-2026.2/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.2 -B/build/reproducible-path/gromacs-2026.2/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.2/build/basic-dp/CMakeFiles 96 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/selection /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/googletest/googletest /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" gtest /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.2-Debian_2026.2_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.2 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.2/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.2/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2026.2-2 -P /build/reproducible-path/gromacs-2026.2/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/googletest/googletest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wundef -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-declarations -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/src/gtest-all.cc [ 0%] Built target scanner /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend [ 0%] Built target mdrun_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/rpc_xdr 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" tng_io_obj make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/basic-dp 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src/gromacs/fmm/CMakeFiles/fmm.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/CMakeFiles/fmm.dir/DependInfo.cmake "--color=" fmm make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/fmm/CMakeFiles/fmm.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 3%] Built target linearalgebra [ 4%] Built target fmm /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/options /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 4%] Built target pulling /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md [ 5%] Built target options /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/DependInfo.cmake "--color=" mpithreads make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build.make src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/build [ 7%] Built target colvars_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/main.cpp.o -MF CMakeFiles/mpithreads.dir/main.cpp.o.d -o CMakeFiles/mpithreads.dir/main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/main.cpp /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build.make src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build.make src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o -MF CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o.d -o CMakeFiles/sync_cyclecount.dir/sync_cyclecount.cpp.o -c 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 7%] Built target sync_cyclecount cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpi_speedtest.dir/multicast.cpp.o -MF CMakeFiles/mpi_speedtest.dir/multicast.cpp.o.d -o CMakeFiles/mpi_speedtest.dir/multicast.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/multicast.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/mpi_speedtest make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 7%] Built target mpi_speedtest cd 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../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/alloc_check.dir/alloc_check.cpp.o -MF CMakeFiles/alloc_check.dir/alloc_check.cpp.o.d -o CMakeFiles/alloc_check.dir/alloc_check.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/alloc_check.cpp /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/taskassignment 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/atomic.cpp.o -MF CMakeFiles/mpithreads.dir/atomic.cpp.o.d -o CMakeFiles/mpithreads.dir/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/atomic.cpp [ 7%] Built target taskassignment cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/cycles.cpp.o -MF CMakeFiles/mpithreads.dir/cycles.cpp.o.d -o CMakeFiles/mpithreads.dir/cycles.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/cycles.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/alloc_check.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 8%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/external/thread_mpi/test/CMakeFiles/mpithreads.dir/split.cpp.o -MF CMakeFiles/mpithreads.dir/split.cpp.o.d -o CMakeFiles/mpithreads.dir/split.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/test/split.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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CMakeFiles/mpithreads.dir/atomic.cpp.o CMakeFiles/mpithreads.dir/cycles.cpp.o CMakeFiles/mpithreads.dir/split.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o ../../../gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -o ../../../../bin/mpithreads make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 9%] Built target mpithreads make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 58%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/gmxapi /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" gmxapi make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && 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target gmxapi make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 60%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/samples 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api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 61%] Built target methane-water-integration [ 61%] Built target argon-forces-integration cd 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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-DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/naming.cpp.o -MF CMakeFiles/testutils-test.dir/naming.cpp.o.d -o CMakeFiles/testutils-test.dir/naming.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/tests/naming.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 62%] Built target testutils-mpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/moduletest.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake "--color=" utility-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f 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src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/alignedallocator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib 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62%] Built target nblib_test_infrastructure cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/DependInfo.cmake "--color=" mpicomm-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/mpicomm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external 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/build/reproducible-path/gromacs-2026.2/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mpicomm-test.dir/link.d "CMakeFiles/mpicomm-test.dir/mpicomm.cpp.o" "CMakeFiles/mpicomm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mpicomm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 62%] Built target mpicomm-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd 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mdrun_test_infrastructure cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem 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/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake "--color=" utility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem 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-MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake "--color=" mdlib-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/naming.cpp.o" "CMakeFiles/testutils-test.dir/posixmemstream.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 64%] Built target testutils-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/coordinate_exception_handling.cpp.o" "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 64%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" awh-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF CMakeFiles/awh-test.dir/awh_setup.cpp.o.d -o CMakeFiles/awh-test.dir/awh_setup.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests/awh_setup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/booltype.cpp /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" density_fitting_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/densityfitting/tests/densityfitting.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include 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/build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external 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/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/bitmask128.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 64%] Built target density_fitting_applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/defaultinitializationallocator.cpp /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" qmmm_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/friction_metric.cpp.o -MF CMakeFiles/awh-test.dir/friction_metric.cpp.o.d -o CMakeFiles/awh-test.dir/friction_metric.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/awh/tests/friction_metric.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/freeenergyparameters.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 64%] Built target awh-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevin.cpp.o -MF CMakeFiles/mdlib-test.dir/langevin.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevin.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/langevin.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/langevintestdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests/qmmmforceproviderstate.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/langevintestrunners.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/message_string_collector.cpp /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" colvars_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mpicomm.cpp.o -MF CMakeFiles/utility-test.dir/mpicomm.cpp.o.d -o CMakeFiles/utility-test.dir/mpicomm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/mpicomm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/path.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceproviderstate.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 65%] Built target qmmm_applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/DependInfo.cmake "--color=" plumed_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/plumed/tests/plumedOptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -MF CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o.d -o CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/parrinellorahman.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/scope_guard.cpp.o -MF CMakeFiles/utility-test.dir/scope_guard.cpp.o.d -o CMakeFiles/utility-test.dir/scope_guard.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/scope_guard.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/plumed_applied_forces-test.dir/link.d "CMakeFiles/plumed_applied_forces-test.dir/plumedOptions.cpp.o" "CMakeFiles/plumed_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/plumed_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 65%] Built target plumed_applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/DependInfo.cmake "--color=" plumed_md-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build.make src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumed_md_test.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/settle.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 66%] Built target colvars_applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/stringutil.cpp /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/DependInfo.cmake "--color=" nnpot_applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build.make src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/nnpot/tests/nnpot.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/settletestrunners.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -MF CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o.d -o CMakeFiles/plumed_md-test.dir/plumedTestUtils.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/plumed/tests/plumedTestUtils.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/plumed/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/plumed/tests/CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/plumed_md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/nnpot/tests/nnpotoptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/plumed_md-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem 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../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 67%] Built target plumed_md-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/nnpot/tests/nnpotforceprovider.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/txtdump.cpp.o -MF CMakeFiles/utility-test.dir/txtdump.cpp.o.d -o CMakeFiles/utility-test.dir/txtdump.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/txtdump.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/nnpot/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/nnpot/tests/CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" applied_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nnpot_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdlib/tests/wholemoleculetransform.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nnpot_applied_forces-test.dir/link.d "CMakeFiles/nnpot_applied_forces-test.dir/nnpot.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotoptions.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpottopologypreprocessor.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/nnpotforceprovider.cpp.o" "CMakeFiles/nnpot_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nnpot_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 67%] Built target nnpot_applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-stringop-truncation -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" listed_forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 67%] Built target applied_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/listed_forces/tests/pairs.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constraintgroupsize.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/langevin.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestdata.cpp.o" "CMakeFiles/mdlib-test.dir/langevintestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/vsite.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 69%] Built target mdlib-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" nbnxm-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/vecdump.cpp.o -MF CMakeFiles/utility-test.dir/vecdump.cpp.o.d -o CMakeFiles/utility-test.dir/vecdump.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/vecdump.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/kernel_test.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/vectypes.cpp.o -MF CMakeFiles/utility-test.dir/vectypes.cpp.o.d -o CMakeFiles/utility-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/utility/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/DependInfo.cmake "--color=" nbnxm-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/pairlist.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-gpu-test.dir/link.d "CMakeFiles/nbnxm-gpu-test.dir/pairlist.cpp.o" "CMakeFiles/nbnxm-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 70%] Built target nbnxm-gpu-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -MF CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o.d -o CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/plainpairlist.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -MF CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o.d -o CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/simd_energy_accumulator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 70%] Built target listed_forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -MF CMakeFiles/nbnxm-test.dir/testsystem.cpp.o.d -o CMakeFiles/nbnxm-test.dir/testsystem.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/testsystem.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/DependInfo.cmake "--color=" nonbonded-fep-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/freeenergykernel.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests/freeenergykernel.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/DependInfo.cmake "--color=" nonbonded-fep-gpu-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o -MF 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-I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/plainpairlist.cpp.o" "CMakeFiles/nbnxm-test.dir/simd_energy_accumulator.cpp.o" "CMakeFiles/nbnxm-test.dir/testsystem.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 70%] Built target nbnxm-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" onlinehelp-test-shared make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-gpu-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nonbonded-fep-gpu-test.dir/link.d "CMakeFiles/nonbonded-fep-gpu-test.dir/freeenergygpukernel.cpp.o" "CMakeFiles/nonbonded-fep-gpu-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-gpu-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 71%] Built target nonbonded-fep-gpu-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include 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CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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"CMakeFiles/nonbonded-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nonbonded-fep-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 71%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 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-DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/mpicomm.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/scope_guard.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/txtdump.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/vecdump.cpp.o" "CMakeFiles/utility-test.dir/vectypes.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 73%] Built target utility-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 73%] Built target domdec-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fft/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" fft-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fft/tests/fft.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 73%] Built target domdec-mpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/tests/pmesplinespreadtest.cpp /usr/bin/make -f src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build.make src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/DependInfo.cmake "--color=" fmm-interface-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build.make src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/tests/fmm_mdpoptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/tests/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/ewald/tests/pme.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fmm/tests/CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -MF CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o.d -o CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/tests/fmmforceprovider.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 73%] Built target fft-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" gpu_utils-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" 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src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/DependInfo.cmake "--color=" gpu_utils-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-mpi-test.dir/build make[4]: 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CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fmm-interface-tests.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fmm-interface-tests.dir/link.d "CMakeFiles/fmm-interface-tests.dir/fmm_mdpoptions.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmm_mdpvalidator.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceprovider.cpp.o" "CMakeFiles/fmm-interface-tests.dir/fmmforceproviderbuilder.cpp.o" "CMakeFiles/fmm-interface-tests.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fmm-interface-tests ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 73%] Built target fmm-interface-tests cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/device_buffer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 73%] Built target ewald-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gpu_utils/tests/hostallocator.cpp /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" hardware-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/hardware/tests/cpuinfo.cpp /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" math-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gpu_utils-mpi-test.dir/link.d "CMakeFiles/gpu_utils-mpi-test.dir/gpu_aware_mpi.cpp.o" "CMakeFiles/gpu_utils-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 75%] Built target gpu_utils-mpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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-c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 [ 75%] Built target hardware-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 75%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" mdspan-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/dofit.cpp /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" mdtypes-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/enerdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/tests/enerdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests/extensions.cpp /usr/bin/c++ 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/usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 75%] Built target gpu_utils-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" onlinehelp-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 76%] Built target mdspan-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" options-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 76%] Built target onlinehelp-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include 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-isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/neldermead.cpp.o -MF CMakeFiles/math-test.dir/neldermead.cpp.o.d -o CMakeFiles/math-test.dir/neldermead.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/neldermead.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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/usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 76%] Built target mdtypes-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" pbcutil-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/tests/com.cpp /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/threefry.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 77%] Built target pbcutil-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" restraintpotential-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 77%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/serialization/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/DependInfo.cmake "--color=" serialization-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build.make src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 77%] Built target random-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/serialization/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/serialization/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/serialization/tests/CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/serialization/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/serialization-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/serialization-test.dir/link.d "CMakeFiles/serialization-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/serialization-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/serialization-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/serialization-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 78%] Built target serialization-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" table-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/tests/usergpuids.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/complex.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 79%] Built target math-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/timing/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" timing-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 80%] Built target timing-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" topology-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 81%] Built target taskassignment-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/exclusionblocks.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 81%] Built target table-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so ../../../../lib/libgtest.so.1.17.0 /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a /usr/lib/riscv64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 81%] Built target pull-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/mtop.cpp /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" simd-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/generate_test_points.cpp.o -MF CMakeFiles/simd-test.dir/generate_test_points.cpp.o.d -o CMakeFiles/simd-test.dir/generate_test_points.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/generate_test_points.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/scalar.cpp /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/compat/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/compat/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" compat-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 81%] Built target compat-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/scalar_math.cpp /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" gmxana-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -MF CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmxanatestbase.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_chi.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 82%] Built target topology-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem 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/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_rms.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 82%] Built target options-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd_vector_operations.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" gmxpreprocess-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/convparm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ 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/build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/simd/tests/simd4_vector_operations.cpp cd 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/generate_test_points.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 83%] Built target simd-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" pdb2gmx1-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmxanatestbase.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rms.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsdist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rmsf.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_sorient.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_rotmat.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_saltbr.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 84%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" pdb2gmx2-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" pdb2gmx3-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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-DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 84%] Built target pdb2gmx1-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 84%] Built target pdb2gmx2-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/correlationfunctions/tests 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include 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CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/correlationfunctions/tests/correlationdataset.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 84%] Built target pdb2gmx3-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem 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CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/solvate.cpp /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake "--color=" coordinateio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 84%] Built target correlations-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/topdirs.cpp /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" energyanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/convparm.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 85%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/outputadapters.cpp /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" tool-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 85%] Built target analysisdata-test-shared cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/tools/tests/helpwriting.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 86%] Built target energyanalysis-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 86%] Built target tool-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" fileio-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make 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-Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/tools/tests/CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/h5md/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/h5md-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/h5md-test.dir/link.d "CMakeFiles/h5md-test.dir/h5md_disabled.cpp.o" "CMakeFiles/h5md-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/h5md.dir/h5md.cpp.o -o ../../../../../bin/h5md-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 ../../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 87%] Built target h5md-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" selection-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test-with-leaks.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c 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../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 88%] Built target coordinateio-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/filemd5.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tool-test-with-leaks.dir/link.d "CMakeFiles/tool-test-with-leaks.dir/convert-tpr-with-leaks.cpp.o" "CMakeFiles/tool-test-with-leaks.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test-with-leaks ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 88%] Built target tool-test-with-leaks cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/filetypes.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" mdrun-output-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/matio.cpp.o -MF CMakeFiles/fileio-test.dir/matio.cpp.o.d -o CMakeFiles/fileio-test.dir/matio.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/matio.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 88%] Built target mdrun-output-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/readinp.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" mdrun-modules-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include 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-isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/timecontrol.cpp.o -MF CMakeFiles/fileio-test.dir/timecontrol.cpp.o.d -o CMakeFiles/fileio-test.dir/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/timecontrol.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o -MF CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o.d -o CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/xdr_serializer.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/xvgio.cpp.o -MF CMakeFiles/fileio-test.dir/xvgio.cpp.o.d -o CMakeFiles/fileio-test.dir/xvgio.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 89%] Built target mdrun-modules-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" mdrun-io-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/checkpoint.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" mdrun-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/awh.cpp.o -MF CMakeFiles/mdrun-test.dir/awh.cpp.o.d -o CMakeFiles/mdrun-test.dir/awh.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/awh.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 89%] Built target selection-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/multiple_time_stepping.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/matio.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xdr_serializer.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 ../../../../lib/libgmock.so.1.17.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 90%] Built target fileio-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/freezegroups.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" mdrun-single-rank-algorithms-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/dispersion_correction.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" minimize-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/orires.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 90%] Built target mdrun-io-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -MF CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o.d -o CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/boxdeformation.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 90%] Built target minimize-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 90%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" mdrun-non-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" mdrun-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 90%] Built target mdrun-tpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem 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../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 91%] Built target mdrun-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external 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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 91%] Built target mdrun-mpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem 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CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/simple_mdrun.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" mdrun-multisim-replex-equivalence-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/replicaexchange_equivalence.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 92%] Built target mdrun-multisim-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 92%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" mdrun-mpi-pme-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem 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/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" mdrun-coordination-basic-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 92%] Built target mdrun-non-integrator-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/periodicactions_basic.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" mdrun-coordination-coupling-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../../../gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat 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'/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 92%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem 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Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 92%] Built target mdrun-coordination-basic-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" mdrun-pull-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f 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src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/pull.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 93%] Built target mdrun-coordination-coupling-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" mdrun-rotation-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 93%] Built target mdrun-coordination-constraints-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" mdrun-simulator-comparison-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/simulator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/expandedensemble.cpp.o" "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 93%] Built target mdrun-fep-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" mdrun-vsites-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/tests/virtualsites.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 94%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" gmxapi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/restraint.cpp.o -MF CMakeFiles/gmxapi-test.dir/restraint.cpp.o.d -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests/restraint.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 94%] Built target mdrun-rotation-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests/status.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 94%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests/stopsignaler.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" workflow-details-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/workflow.cpp.o -MF CMakeFiles/workflow-details-test.dir/workflow.cpp.o.d -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/workflow/tests/workflow.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 94%] Built target mdrun-vsites-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests/system.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake "--color=" nblib-integrator-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat 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/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" nblib-setup-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/gmxapi/cpp/tests/version.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.17.0 ../../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 95%] Built target workflow-details-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem 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CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 95%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" nblib-tpr-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/tpr.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" nblib-integration-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/molecules.cpp /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" nblib-listed-forces-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 96%] Built target nblib-tpr-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/tests/virials.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/typetests.cpp /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib/util/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/util/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" nblib-util-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/util/tests/traits.cpp /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" commandline-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 96%] Built target nblib-util-test cd 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-I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/calculator.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp 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-I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -MF CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests/plainpairlistranges.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.17.0 ../../../lib/libgtest.so.1.17.0 ../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 97%] Built target nblib-setup-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" mdrunutility-mpi-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/plainpairlistranges.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 97%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2026.2/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlineparser.cpp /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" analysisdata-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 97%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/nblib/tests -I/build/reproducible-path/gromacs-2026.2/api/nblib/include -I/build/reproducible-path/gromacs-2026.2/api/nblib -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" trajectoryanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include 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CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/pargs.cpp.o -MF CMakeFiles/commandline-test.dir/pargs.cpp.o.d -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/commandline/tests/pargs.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 97%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/arraydata.cpp /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/api/nblib /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" nblib-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 97%] Built target nblib-tests cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/histogram.cpp.o -MF CMakeFiles/analysisdata-test.dir/histogram.cpp.o.d -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/histogram.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/dssp.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 98%] Built target commandline-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem 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-DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/gyrate.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/hbond.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [ 98%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/testutils/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/external/muparser -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2026.2/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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"CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.11.0.0 /usr/lib/riscv64-linux-gnu/libm.so /usr/lib/gcc/riscv64-linux-gnu/15/libgomp.so /lib/riscv64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.17.0 ../../../../lib/libgtest.so.1.17.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' cd /build/reproducible-path/gromacs-2026.2/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp /build/reproducible-path/gromacs-2026.2/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake "--color=" tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.2/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2026.2/build/basic-dp/lib ctest -V -E MdlibUnitTest) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2026.2/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2026.2/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2026.2/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -136479279 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.049 0.025 199.2 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 20.599 1.165 8.192 0.001 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1140 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1091174933 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.085 0.043 199.5 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 11.888 2.019 14.195 0.001 1: [ OK ] GmxApiTest.RunnerBasicMD (1102 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -1083191555 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.087 0.043 199.6 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 81.488 0.295 2.071 0.004 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.015 0.007 197.7 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 482.458 0.050 0.350 0.023 1: [ OK ] GmxApiTest.RunnerReinitialize (1110 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -46347875 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.086 0.043 199.5 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 11.753 2.042 14.358 0.001 1: trr version: GMX_trn_file (double precision) 1: 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.012 0.006 198.2 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 82.078 0.292 2.056 0.004 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (1104 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -492545 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.090 0.045 199.5 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 18.647 1.287 9.050 0.001 1: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.014 0.007 197.4 1: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 1: Performance: 46.998 0.511 3.591 0.002 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (1123 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -536873771 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (1035 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (6618 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (6637 ms total) 1: [ PASSED ] 9 tests. 1/103 Test #1: GmxapiExternalInterfaceTests .............. Passed 6.69 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -571932678 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (1009 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -1744961541 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (982 ms) 2: [----------] 2 tests from GmxApiTest (1992 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (2008 ms total) 2: [ PASSED ] 2 tests. 2/103 Test #2: GmxapiInternalInterfaceTests .............. Passed 2.04 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (35 ms) 3: [----------] 8 tests from NBlibTest (37 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (2 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (2 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (2 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (0 ms) 3: [----------] 1 test from LinearChainDataFixture (0 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (47 ms total) 3: [ PASSED ] 44 tests. 3/103 Test #3: NbLibListedForcesTests .................... Passed 0.11 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/103 Test #4: NbLibSamplesTestArgon ..................... Passed 0.03 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 5/103 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.03 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (1 ms total) 6: [ PASSED ] 16 tests. 6/103 Test #6: NbLibUtilTests ............................ Passed 0.03 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (3 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (4 ms total) 7: [ PASSED ] 57 tests. 7/103 Test #7: NbLibSetupTests ........................... Passed 0.05 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (10 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (10 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (10 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 2 NOTEs 8: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (10 ms) 8: [----------] 4 tests from TprReaderTest (42 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (58 ms total) 8: [ PASSED ] 4 tests. 8/103 Test #8: NbLibTprTests ............................. Passed 0.09 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (37 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (45 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (45 ms total) 9: [ PASSED ] 20 tests. 9/103 Test #9: NbLibIntegrationTests ..................... Passed 0.07 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/103 Test #10: NbLibIntegratorTests ...................... Passed 0.03 sec test 11 Start 11: threadMPI-mpithreads 11: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mpithreads "-nt" "3" 11: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test 11: Test timeout computed to be: 1500 11: 11: thread_mpi tester. 11: 11: Number of threads: 3 11: 11: thread 0: got arg 10; total number of hw threads: 4 11: thread 2: got arg 10; total number of hw threads: 4 11: thread 1: got arg 10; total number of hw threads: 4 11: my rank = 1 11: my rank = 2 11: my rank = 0 11: Setting thread affinity 11: Testing atomic functions.. 11: OK. 11: Starting tMPI_Thread_cond_signal test: 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 1: 1000 11: processed by thread 2: 0 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 669 11: processed by thread 2: 331 11: tMPI_Thread_cond_signal test: OK 11: processed by thread 0: 588 11: processed by thread 1: 412 11: 11: Starting tMPI_Thread_cond_broadcast test: 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 1: 795 11: processed by thread 2: 1205 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 1032 11: processed by thread 2: 968 11: tMPI_Thread_cond_broadcast test: OK 11: processed by thread 0: 946 11: processed by thread 1: 1054 11: 11: 11: sizeof(atomic_t) = 4, sizeof(atomic_t_ptr)=8, sizeof(spinlock)=4 11: Testing spinlocks.. 11: OK. 11: 11: Testing locks.. 11: OK. 11: 11: Barrier data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Starting MPI_Send and MPI_Recv tests 11: Received: 'From thread 1 to 0: hello.' 11: Received: 'From thread 2 to 0: hello.' 11: Received: 'From thread 1 to 1: hello.' 11: Received: 'From thread 2 to 1: hello.' 11: 11: Starting MPI_Sendrecv tests 11: Received: 'Sendrecv hello, from thread 1' 11: Received: 'Sendrecv hello, from thread 2' 11: Received: 'Sendrecv hello, from thread 0' 11: 11: Starting MPI_Isend/MPI_Irecv tests 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 0 to right (0) from 2', From right: 'Msg 0 to left (0) from 1' 11: From left: 'Msg 0 to right (2) from 1', From right: 'Msg 0 to left (1) from 2' 11: From left: 'Msg 0 to right (1) from 0', From right: 'Msg 0 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 1 to right (0) from 2', From right: 'Msg 1 to left (0) from 1' 11: From left: 'Msg 1 to right (2) from 1', From right: 'Msg 1 to left (1) from 2' 11: From left: 'Msg 1 to right (1) from 0', From right: 'Msg 1 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 2 to right (0) from 2', From right: 'Msg 2 to left (0) from 1' 11: From left: 'Msg 2 to right (2) from 1', From right: 'Msg 2 to left (1) from 2' 11: From left: 'Msg 2 to right (1) from 0', From right: 'Msg 2 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 3 to right (0) from 2', From right: 'Msg 3 to left (0) from 1' 11: From left: 'Msg 3 to right (2) from 1', From right: 'Msg 3 to left (1) from 2' 11: From left: 'Msg 3 to right (1) from 0', From right: 'Msg 3 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 4 to right (0) from 2', From right: 'Msg 4 to left (0) from 1' 11: From left: 'Msg 4 to right (2) from 1', From right: 'Msg 4 to left (1) from 2' 11: From left: 'Msg 4 to right (1) from 0', From right: 'Msg 4 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 5 to right (0) from 2', From right: 'Msg 5 to left (0) from 1' 11: From left: 'Msg 5 to right (2) from 1', From right: 'Msg 5 to left (1) from 2' 11: From left: 'Msg 5 to right (1) from 0', From right: 'Msg 5 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 6 to right (0) from 2', From right: 'Msg 6 to left (0) from 1' 11: From left: 'Msg 6 to right (2) from 1', From right: 'Msg 6 to left (1) from 2' 11: From left: 'Msg 6 to right (1) from 0', From right: 'Msg 6 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 7 to right (0) from 2', From right: 'Msg 7 to left (0) from 1' 11: From left: 'Msg 7 to right (2) from 1', From right: 'Msg 7 to left (1) from 2' 11: From left: 'Msg 7 to right (1) from 0', From right: 'Msg 7 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 8 to right (0) from 2', From right: 'Msg 8 to left (0) from 1' 11: From left: 'Msg 8 to right (2) from 1', From right: 'Msg 8 to left (1) from 2' 11: From left: 'Msg 8 to right (1) from 0', From right: 'Msg 8 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: From left: 'Msg 9 to right (0) from 2', From right: 'Msg 9 to left (0) from 1' 11: From left: 'Msg 9 to right (2) from 1', From right: 'Msg 9 to left (1) from 2' 11: From left: 'Msg 9 to right (1) from 0', From right: 'Msg 9 to left (2) from 0' 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Async data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Split test 11: I'm in world rank 0, and have new rank 1 in group 0x555599aa11c0 of size 2 11: 11: Starting MPI_Split test 11: I'm in world rank 1, and have new rank 0 in group 0x555599aa1720 of size 1 11: I'm in world rank 2, and have new rank 0 in group 0x555599aa11c0 of size 2 11: I'm in world rank 0, and have new rank 0 in group 0x555599aa1b60 of size 1 11: my rank is 0, MPI_Comm_compare said: 3 11: I'm in world rank 1, and have new rank 0 in group 0x555599aa1dd0 of size 1 11: 11: Starting MPI_Split test 11: my rank is 1, MPI_Comm_compare said: 3 11: I'm in world rank 2, and have new rank 0 in group 0x555599aa2120 of size 1 11: my rank is 2, MPI_Comm_compare said: 3 11: I'm in world rank 0, and have new rank 2 in group 0x555599aa1b60 of size 3 11: my rank is 0, MPI_Comm_compare said: 2 11: Starting repeated MPI_Split() test. 11: I'm in world rank 1, and have new rank 1 in group 0x555599aa1b60 of size 3 11: my rank is 1, MPI_Comm_compare said: 2 11: I'm in world rank 2, and have new rank 0 in group 0x555599aa1b60 of size 3 11: my rank is 2, MPI_Comm_compare said: 2 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: Done. 11: 11: Starting MPI_Bcast test 11: Received: 'Broadcast message 0 from 0' 11: Received: 'Broadcast message 0 from 1' 11: Received: 'Broadcast message 0 from 2' 11: Received: 'Broadcast message 1 from 0' 11: Received: 'Broadcast message 1 from 1' 11: Received: 'Broadcast message 1 from 2' 11: Broadcast data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Gather test 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: Received: 'Gather message 00 from 000 11: Gather message 00 from 001 11: Gather message 00 from 002 11: ' 11: Gather data test: 11: Received: 'Gather message 01 from 000 11: Gather message 01 from 001 11: Gather message 01 from 002 11: ' 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Gatherv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Scatter test 11: Received from 0: 'Scatter message from 000 to 000' 11: Received back from 1: 'Scatter message from 000 to 001' 11: Received back from 2: 'Scatter message from 000 to 002' 11: Scatter data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: Scatterv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Alltoall test 11: From 0: 0->0(0) 1->0(0) 2->0(0) 11: From 1: 0->1(0) 1->1(0) 2->1(0) 11: From 2: 0->2(0) 1->2(0) 2->2(0) 11: From 0: 0->0(1) 1->0(1) 2->0(1) 11: From 1: 0->1(1) 1->1(1) 2->1(1) 11: From 2: 0->2(1) 1->2(1) 2->2(1) 11: From 0: 0->0(2) 1->0(2) 2->0(2) 11: From 1: 0->1(2) 1->1(2) 2->1(2) 11: From 2: 0->2(2) 1->2(2) 2->2(2) 11: From 0: 0->0(3) 1->0(3) 2->0(3) 11: From 1: 0->1(3) 1->1(3) 2->1(3) 11: From 2: 0->2(3) 1->2(3) 2->2(3) 11: Alltoallv data test: 11: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 11: OK. 11: 11: Starting MPI_Reduce test 11: again: my rank = 2 11: Results from mpi_reduce: 11: (0: 2 == 2): OK 11: (1: 5 == 5): OK 11: (2: 8 == 8): OK 11: (3: 11 == 11): OK 11: (4: 14 == 14): OK 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 1 11: again: my rank = 0 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 1: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: Results from mpi_allreduce process 2: 11: (5: 4080 == 4080): OK 11: (6: 6840 == 6840): OK 11: (7: 10626 == 10626): OK 11: (8: 15600 == 15600): OK 11: (9: 21924 == 21924): OK 11: again: my rank = 2 11: again: my rank = 1 11: again: my rank = 0 11: 11: Starting tMPI_Allreduce test 11: Results from mpi_allreduce process 0: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 1: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: Results from mpi_allreduce process 2: 11: (5: 17 == 17): OK 11: (6: 20 == 20): OK 11: (7: 23 == 23): OK 11: (8: 26 == 26): OK 11: (9: 29 == 29): OK 11: again: my rank = 2 11: again: my rank = 1 11: again: my rank = 0 11: 11: Starting tMPI_Scan test 11: Results from mpi_scan process 0: 11: OK 11: again: my rank = 2 11: again: my rank = 0 11: again: my rank = 1 11: 11: Starting tMPI_Once test 11: Printing this number once: 0 (my rank=1) 11: Printing this number once: 2 (my rank=0) 11: Printing this number once: 3 (my rank=0) 11: Printing this number once: 4 (my rank=0) 11: Printing this number once: 5 (my rank=0) 11: Printing this number once: 6 (my rank=0) 11: Printing this number once: 7 (my rank=0) 11: Printing this number once: 8 (my rank=0) 11: Printing this number once: 9 (my rank=0) 11: Done. 11: 11: Printing this number once: 1 (my rank=2) 11: I was first for 0, my rank=1 11: Finishing.. 11/103 Test #11: threadMPI-mpithreads ...................... Passed 14.83 sec test 12 Start 12: threadMPI-sync_cyclecount 12: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/sync_cyclecount "2" "0" "1" 12: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test 12: Test timeout computed to be: 1500 12: 12: sync_cyclecount. 12: 12: Number of threads: 3 12: 12: Number of counters: 3 12: 12: No cycle count. 12/103 Test #12: threadMPI-sync_cyclecount ................. Passed 0.00 sec test 13 Start 13: threadMPI-mpi_speedtest 13: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mpi_speedtest "-nt" "3" 13: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test 13: Test timeout computed to be: 1500 13: No cycle count. 13: No cycle count. 13: No cycle count. 13/103 Test #13: threadMPI-mpi_speedtest ................... Passed 0.00 sec test 14 Start 14: threadMPI-notmpi 14: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/notmpi "-nt" "3" 14: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test 14: Test timeout computed to be: 1500 14: 14: notmpi. 14: 14: Number of threads: 3 14: 14: This platform supports setting thread affinity 14: My ID=1, i=1000, tid=0x7fffb8000be0 14: My ID=0, i=1000, tid=0x55559a19c5d0 14: My ID=2, i=1000, tid=0x7fffb0000be0 14: Total count: 3000 14/103 Test #14: threadMPI-notmpi .......................... Passed 0.01 sec test 15 Start 15: threadMPI-alloc_check 15: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/alloc_check "-nt" "3" 15: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/external/thread_mpi/test 15: Test timeout computed to be: 1500 15: 15: Memory (de)allocation tester. 15: 15: Number of threads: 3 15: 15: thread 2: got arg 10; total number of hw threads: 4 15: my rank = 2 15: thread 0: got arg 10; total number of hw threads: 4 15: my rank = 0 15: thread 1: got arg 10; total number of hw threads: 4 15: my rank = 1 15: 15: Starting MPI_Sendrecv tests 15: Received: 'Sendrecv hello, from thread 1' 15: Received: 'Sendrecv hello, from thread 2' 15: Received: 'Sendrecv hello, from thread 0' 15: 15: Starting MPI_Bcast test 15: Received: 'Broadcast message 0 from 0' 15: Received: 'Broadcast message 0 from 1' 15: Received: 'Broadcast message 0 from 2' 15: Received: 'Broadcast message 1 from 0' 15: Received: 'Broadcast message 1 from 1' 15: Received: 'Broadcast message 1 from 2' 15: 15: Starting MPI_Gather test 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15: Received: 'Gather message 00 from 000 15: Gather message 00 from 001 15: Gather message 00 from 002 15: ' 15: Finishing.. 15: Received: 'Gather message 01 from 000 15: Gather message 01 from 001 15: Gather message 01 from 002 15: ' 15/103 Test #15: threadMPI-alloc_check ..................... Passed 0.00 sec test 16 Start 16: TestUtilsUnitTests 16: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/testutils/tests 16: Test timeout computed to be: 30 16: [==========] Running 81 tests from 8 test suites. 16: [----------] Global test environment set-up. 16: [----------] 10 tests from InteractiveTestHelperTest 16: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 16: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 16: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 16: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 16: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 16: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 16: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 16: [----------] 10 tests from InteractiveTestHelperTest (6 ms total) 16: 16: [----------] 10 tests from NameOfTestFromTupleTest 16: [ RUN ] NameOfTestFromTupleTest.WorksWithEmptyTuple 16: [ OK ] NameOfTestFromTupleTest.WorksWithEmptyTuple (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunction 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctionOfEnumVariable (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction 16: [ OK ] NameOfTestFromTupleTest.RejectsNullptrFormatFunction (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatLambda 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatLambda (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithUseStringFormat 16: [ OK ] NameOfTestFromTupleTest.WorksWithUseStringFormat (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithPrefixFormatter 16: [ OK ] NameOfTestFromTupleTest.WorksWithPrefixFormatter (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFunctor 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFunctor (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray 16: [ OK ] NameOfTestFromTupleTest.WorksWithFormatFromEnumerationArray (0 ms) 16: [ RUN ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters 16: [ OK ] NameOfTestFromTupleTest.WorksWithMixtureOfFormatters (0 ms) 16: [----------] 10 tests from NameOfTestFromTupleTest (0 ms total) 16: 16: [----------] 3 tests from RefDataFilenameMakerTest 16: [ RUN ] RefDataFilenameMakerTest.WorksWithFormatFunction 16: [ OK ] RefDataFilenameMakerTest.WorksWithFormatFunction (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters 16: [ OK ] RefDataFilenameMakerTest.WorksWithMixtureOfFormatters (0 ms) 16: [ RUN ] RefDataFilenameMakerTest.WorksWithToEmpty 16: [ OK ] RefDataFilenameMakerTest.WorksWithToEmpty (0 ms) 16: [----------] 3 tests from RefDataFilenameMakerTest (0 ms total) 16: 16: [----------] 6 tests from PosixMemstreamTest 16: [ RUN ] PosixMemstreamTest.ConstructsAndDestructs 16: [ OK ] PosixMemstreamTest.ConstructsAndDestructs (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilClosed 16: [ OK ] PosixMemstreamTest.HasAStreamUntilClosed (0 ms) 16: [ RUN ] PosixMemstreamTest.CanFetchString 16: [ OK ] PosixMemstreamTest.CanFetchString (0 ms) 16: [ RUN ] PosixMemstreamTest.HasAStreamUntilStringIsFetched 16: [ OK ] PosixMemstreamTest.HasAStreamUntilStringIsFetched (0 ms) 16: [ RUN ] PosixMemstreamTest.CanWriteToStream 16: [ OK ] PosixMemstreamTest.CanWriteToStream (0 ms) 16: [ RUN ] PosixMemstreamTest.CanCheckBufferWithContents 16: [ OK ] PosixMemstreamTest.CanCheckBufferWithContents (0 ms) 16: [----------] 6 tests from PosixMemstreamTest (0 ms total) 16: 16: [----------] 37 tests from ReferenceDataTest 16: [ RUN ] ReferenceDataTest.HandlesSimpleData 16: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 16: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 16: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringBlockData 16: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesVectorData 16: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceData 16: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRef 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRef (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData 16: [ OK ] ReferenceDataTest.CheckSequenceArrayRefHandlesSequenceOfCustomData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectData 16: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 16: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingData 16: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedData 16: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 16: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnys 16: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 16: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 16: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 16: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 16: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 16: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 16: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 16: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 16: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 16: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 16: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 16: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesReadingValues 16: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 16: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 16: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 16: [----------] 37 tests from ReferenceDataTest (12 ms total) 16: 16: [----------] 7 tests from FloatingPointDifferenceTest 16: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 16: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 16: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 16: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 16: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 16: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 16: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 16: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 16: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 16: 16: [----------] 4 tests from FloatingPointToleranceTest 16: [ RUN ] FloatingPointToleranceTest.UlpTolerance 16: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 16: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 16: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 16: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 16: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 16: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 16: 16: [----------] 4 tests from XvgTests 16: [ RUN ] XvgTests.CreateFile 16: [ OK ] XvgTests.CreateFile (0 ms) 16: [ RUN ] XvgTests.CheckMissing 16: [ OK ] XvgTests.CheckMissing (0 ms) 16: [ RUN ] XvgTests.CheckExtra 16: [ OK ] XvgTests.CheckExtra (0 ms) 16: [ RUN ] XvgTests.ReadIncorrect 16: [ OK ] XvgTests.ReadIncorrect (0 ms) 16: [----------] 4 tests from XvgTests (2 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 81 tests from 8 test suites ran. (21 ms total) 16: [ PASSED ] 81 tests. 16/103 Test #16: TestUtilsUnitTests ........................ Passed 0.05 sec test 17 Start 17: TestUtilsMpiUnitTests 17: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/testutils/tests 17: Test timeout computed to be: 30 17: [==========] Running 3 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 1 test from MpiSelfTest 17: [ RUN ] MpiSelfTest.Runs 17: [ OK ] MpiSelfTest.Runs (0 ms) 17: [----------] 1 test from MpiSelfTest (0 ms total) 17: 17: [----------] 2 tests from MpiRefDataTest 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRank (1 ms) 17: [ RUN ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName 17: [ OK ] MpiRefDataTest.UsesDifferentReferenceDataOnEachRankWithCustomName (0 ms) 17: [----------] 2 tests from MpiRefDataTest (1 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 3 tests from 2 test suites ran. (2 ms total) 17: [ PASSED ] 3 tests. 17/103 Test #17: TestUtilsMpiUnitTests ..................... Passed 0.03 sec test 18 Start 18: UtilityUnitTests 18: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 18: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests 18: Test timeout computed to be: 30 18: [==========] Running 495 tests from 68 test suites. 18: [----------] Global test environment set-up. 18: [----------] 6 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/0.Comparison 18: [ OK ] AllocatorTest/0.Comparison (0 ms) 18: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/0.Move 18: [ OK ] AllocatorTest/0.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/0 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/1.Comparison 18: [ OK ] AllocatorTest/1.Comparison (0 ms) 18: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/1.Move 18: [ OK ] AllocatorTest/1.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/1 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/2.Comparison 18: [ OK ] AllocatorTest/2.Comparison (0 ms) 18: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/2.Move 18: [ OK ] AllocatorTest/2.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/2 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 18: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/3.Comparison 18: [ OK ] AllocatorTest/3.Comparison (0 ms) 18: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/3.Move 18: [ OK ] AllocatorTest/3.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/3 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/4, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/4.Comparison 18: [ OK ] AllocatorTest/4.Comparison (0 ms) 18: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/4.Move 18: [ OK ] AllocatorTest/4.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/4 (0 ms total) 18: 18: [----------] 6 tests from AllocatorTest/5, where TypeParam = gmx::Allocator,gmx::PageAlignedAllocationPolicy> 18: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 18: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 18: [ RUN ] AllocatorTest/5.Comparison 18: [ OK ] AllocatorTest/5.Comparison (0 ms) 18: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 18: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 18: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 18: [ RUN ] AllocatorTest/5.Move 18: [ OK ] AllocatorTest/5.Move (0 ms) 18: [----------] 6 tests from AllocatorTest/5 (0 ms total) 18: 18: [----------] 1 test from AllocatorUntypedTest 18: [ RUN ] AllocatorUntypedTest.Comparison 18: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 18: [----------] 1 test from AllocatorUntypedTest (0 ms total) 18: 18: [----------] 4 tests from EmptyArrayRefTest 18: [ RUN ] EmptyArrayRefTest.IsEmpty 18: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 18: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 18: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 18: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 18: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 18: 18: [----------] 1 test from EmptyConstArrayRefTest 18: [ RUN ] EmptyConstArrayRefTest.IsEmpty 18: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 18: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 18: 18: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 18: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 18: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 18: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 18: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 18: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 18: 18: [----------] 8 tests from BoolType 18: [ RUN ] BoolType.ImplicitConversion 18: [ OK ] BoolType.ImplicitConversion (0 ms) 18: [ RUN ] BoolType.FalseByDefault 18: [ OK ] BoolType.FalseByDefault (0 ms) 18: [ RUN ] BoolType.Assignment 18: [ OK ] BoolType.Assignment (0 ms) 18: [ RUN ] BoolType.Copy 18: [ OK ] BoolType.Copy (0 ms) 18: [ RUN ] BoolType.ArrayRefCanBeCreated 18: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 18: [ RUN ] BoolType.CanBeCastToBool 18: [ OK ] BoolType.CanBeCastToBool (0 ms) 18: [ RUN ] BoolType.HasSizeOfBool 18: [ OK ] BoolType.HasSizeOfBool (0 ms) 18: [ RUN ] BoolType.HasAlignmentOfBool 18: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 18: [----------] 8 tests from BoolType (0 ms total) 18: 18: [----------] 4 tests from ArrayRefFromBoolTypeVector 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.Works 18: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 18: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 18: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 18: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 18: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 18: 18: [----------] 7 tests from CStringUtilityTest 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 18: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 18: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 18: [ RUN ] CStringUtilityTest.strip_comment 18: [ OK ] CStringUtilityTest.strip_comment (0 ms) 18: [ RUN ] CStringUtilityTest.upstring 18: [ OK ] CStringUtilityTest.upstring (0 ms) 18: [ RUN ] CStringUtilityTest.ltrim 18: [ OK ] CStringUtilityTest.ltrim (0 ms) 18: [ RUN ] CStringUtilityTest.rtrim 18: [ OK ] CStringUtilityTest.rtrim (0 ms) 18: [ RUN ] CStringUtilityTest.trim 18: [ OK ] CStringUtilityTest.trim (0 ms) 18: [----------] 7 tests from CStringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from DefaultInitializationAllocator 18: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 18: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 18: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 18: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 18: 18: [----------] 4 tests from EnumerationHelpersTest 18: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 18: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 18: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 18: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 18: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 18: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 18: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 18: 18: [----------] 1 test from EnumClassSuitsEnumerationArray 18: [ RUN ] EnumClassSuitsEnumerationArray.Works 18: [ OK ] EnumClassSuitsEnumerationArray.Works (0 ms) 18: [----------] 1 test from EnumClassSuitsEnumerationArray (0 ms total) 18: 18: [----------] 18 tests from FixedCapacityVectorTest 18: [ RUN ] FixedCapacityVectorTest.IsEmpty 18: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstructorWorks 18: [ OK ] FixedCapacityVectorTest.ConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PushWorks 18: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.PopWorks 18: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ResizeWorks 18: [ OK ] FixedCapacityVectorTest.ResizeWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ClearWorks 18: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 18: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.AtThrows 18: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 18: [ RUN ] FixedCapacityVectorTest.IteratorWorks 18: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 18: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 18: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyConstructorWorks 18: [ OK ] FixedCapacityVectorTest.CopyConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.CopyAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveConstructorWorks 18: [ OK ] FixedCapacityVectorTest.MoveConstructorWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.MoveAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ElementAssignmentWorks 18: [ OK ] FixedCapacityVectorTest.ElementAssignmentWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.DataWorks 18: [ OK ] FixedCapacityVectorTest.DataWorks (0 ms) 18: [ RUN ] FixedCapacityVectorTest.ConstMethodsWork 18: [ OK ] FixedCapacityVectorTest.ConstMethodsWork (0 ms) 18: [----------] 18 tests from FixedCapacityVectorTest (0 ms total) 18: 18: [----------] 7 tests from TreeValueTransformTest 18: [ RUN ] TreeValueTransformTest.SimpleTransforms 18: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 18: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 18: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 18: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromString 18: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 18: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 18: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 18: [ RUN ] TreeValueTransformTest.ScopedTransformRules 18: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 18: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 18: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 18: [----------] 7 tests from TreeValueTransformTest (3 ms total) 18: 18: [----------] 1 test from TreeValueTransformErrorTest 18: [ RUN ] TreeValueTransformErrorTest.ConversionError 18: [ OK ] TreeValueTransformErrorTest.ConversionError (2 ms) 18: [----------] 1 test from TreeValueTransformErrorTest (2 ms total) 18: 18: [----------] 9 tests from ListOfLists 18: [ RUN ] ListOfLists.EmptyListOfListsWorks 18: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 18: [ RUN ] ListOfLists.AppendWorks 18: [ OK ] ListOfLists.AppendWorks (0 ms) 18: [ RUN ] ListOfLists.EmptyListWorks 18: [ OK ] ListOfLists.EmptyListWorks (0 ms) 18: [ RUN ] ListOfLists.AppendAccessWorks 18: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 18: [ RUN ] ListOfLists.ClearWorks 18: [ OK ] ListOfLists.ClearWorks (0 ms) 18: [ RUN ] ListOfLists.OutOfRangeAccessThrows 18: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 18: [ RUN ] ListOfLists.FrontAndBackWork 18: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 18: [ RUN ] ListOfLists.ExtractsAndRestores 18: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 18: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 18: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 18: [----------] 9 tests from ListOfLists (0 ms total) 18: 18: [----------] 7 tests from LoggerTest 18: [ RUN ] LoggerTest.EmptyLoggerWorks 18: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToStream 18: [ OK ] LoggerTest.LogsToStream (0 ms) 18: [ RUN ] LoggerTest.LogsToFile 18: [ OK ] LoggerTest.LogsToFile (0 ms) 18: [ RUN ] LoggerTest.LevelFilteringWorks 18: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleStreams 18: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 18: [ RUN ] LoggerTest.LogsToMultipleFiles 18: [ OK ] LoggerTest.LogsToMultipleFiles (1 ms) 18: [ RUN ] LoggerTest.LogsToStreamAndFile 18: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 18: [----------] 7 tests from LoggerTest (3 ms total) 18: 18: [----------] 7 tests from MessageStringCollectorTest 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 18: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 18: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 18: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 18: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 18: [ RUN ] MessageStringCollectorTest.CanMoveAssign 18: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 18: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 18: 18: [----------] 12 tests from MpiComm 18: [ RUN ] MpiComm.SingleRankNoComm 18: [ OK ] MpiComm.SingleRankNoComm (0 ms) 18: [ RUN ] MpiComm.CommWorld 18: [ OK ] MpiComm.CommWorld (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: ./src/gromacs/utility/tests/mpicomm.cpp:160: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:168: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:181: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (0 ms) 18: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: ./src/gromacs/utility/tests/mpicomm.cpp:194: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (0 ms) 18: [ RUN ] MpiComm.ConstructorThrowsOnNull 18: ./src/gromacs/utility/tests/mpicomm.cpp:206: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull (0 ms) 18: [ RUN ] MpiComm.CopyConstructorWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:220: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.CopyConstructorWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:243: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorks (0 ms) 18: [ RUN ] MpiComm.AssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:259: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorks 18: ./src/gromacs/utility/tests/mpicomm.cpp:281: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks (0 ms) 18: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 18: ./src/gromacs/utility/tests/mpicomm.cpp:298: Skipped 18: Test skipped because 4 ranks are required 18: 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf (0 ms) 18: [----------] 12 tests from MpiComm (0 ms total) 18: 18: [----------] 1 test from PathTest 18: [ RUN ] PathTest.StripSourcePrefixWorks 18: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 18: [----------] 1 test from PathTest (0 ms total) 18: 18: [----------] 2 tests from PhysicalNodeCommunicatorTest 18: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 18: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 18: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 18: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 18: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 18: 18: [----------] 5 tests from Range 18: [ RUN ] Range.EmptyRangeWorks 18: [ OK ] Range.EmptyRangeWorks (0 ms) 18: [ RUN ] Range.NonEmptyRangeWorks 18: [ OK ] Range.NonEmptyRangeWorks (0 ms) 18: [ RUN ] Range.BeginEnd 18: [ OK ] Range.BeginEnd (0 ms) 18: [ RUN ] Range.IsInRangeWorks 18: [ OK ] Range.IsInRangeWorks (0 ms) 18: [ RUN ] Range.IteratorWorks 18: [ OK ] Range.IteratorWorks (0 ms) 18: [----------] 5 tests from Range (0 ms total) 18: 18: [----------] 3 tests from ScopeGuardTest 18: [ RUN ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit 18: [ OK ] ScopeGuardTest.ScopeGuardExecutesCallbackOnExit (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardCanFreePointers 18: [ OK ] ScopeGuardTest.ScopeGuardCanFreePointers (0 ms) 18: [ RUN ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions 18: [ OK ] ScopeGuardTest.ScopeGuardsCanBeCreatedByHelperFunctions (0 ms) 18: [----------] 3 tests from ScopeGuardTest (0 ms total) 18: 18: [----------] 7 tests from StringConvert 18: [ RUN ] StringConvert.NoResultFromEptyString 18: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 18: [ RUN ] StringConvert.ThreeFloatsSuccessfully 18: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 18: [ RUN ] StringConvert.OneIntSucessfully 18: [ OK ] StringConvert.OneIntSucessfully (0 ms) 18: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 18: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 18: [ RUN ] StringConvert.ThrowsWhenWrongSize 18: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 18: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 18: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 18: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 18: [----------] 7 tests from StringConvert (0 ms total) 18: 18: [----------] 7 tests from StringToEnumValueConverterTest 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 18: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 18: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 18: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 18: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 18: 18: [----------] 9 tests from StringUtilityTest 18: [ RUN ] StringUtilityTest.StartsWith 18: [ OK ] StringUtilityTest.StartsWith (0 ms) 18: [ RUN ] StringUtilityTest.EndsWith 18: [ OK ] StringUtilityTest.EndsWith (0 ms) 18: [ RUN ] StringUtilityTest.StripSuffixIfPresent 18: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 18: [ RUN ] StringUtilityTest.StripString 18: [ OK ] StringUtilityTest.StripString (0 ms) 18: [ RUN ] StringUtilityTest.SplitString 18: [ OK ] StringUtilityTest.SplitString (0 ms) 18: [ RUN ] StringUtilityTest.SplitDelimitedString 18: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 18: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 18: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 18: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 18: [----------] 9 tests from StringUtilityTest (0 ms total) 18: 18: [----------] 2 tests from FormatStringTest 18: [ RUN ] FormatStringTest.HandlesBasicFormatting 18: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 18: [ RUN ] FormatStringTest.HandlesLongStrings 18: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 18: [----------] 2 tests from FormatStringTest (0 ms total) 18: 18: [----------] 1 test from StringFormatterTest 18: [ RUN ] StringFormatterTest.HandlesBasicFormatting 18: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 18: [----------] 1 test from StringFormatterTest (0 ms total) 18: 18: [----------] 1 test from formatAndJoinTest 18: [ RUN ] formatAndJoinTest.Works 18: [ OK ] formatAndJoinTest.Works (0 ms) 18: [----------] 1 test from formatAndJoinTest (0 ms total) 18: 18: [----------] 1 test from JoinStringsTest 18: [ RUN ] JoinStringsTest.Works 18: [ OK ] JoinStringsTest.Works (0 ms) 18: [----------] 1 test from JoinStringsTest (0 ms total) 18: 18: [----------] 6 tests from ReplaceAllTest 18: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 18: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesNoMatches 18: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 18: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 18: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 18: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 18: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 18: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 18: [----------] 6 tests from ReplaceAllTest (0 ms total) 18: 18: [----------] 10 tests from TextLineWrapperTest 18: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 18: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 18: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 18: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectly 18: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndent 18: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 18: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 18: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 18: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 18: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 18: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 18: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 18: [----------] 10 tests from TextLineWrapperTest (2 ms total) 18: 18: [----------] 1 test from PrettyPrintListAsRangeTest 18: [ RUN ] PrettyPrintListAsRangeTest.Works 18: [ OK ] PrettyPrintListAsRangeTest.Works (0 ms) 18: [----------] 1 test from PrettyPrintListAsRangeTest (0 ms total) 18: 18: [----------] 1 test from CompileTimeStringJoin 18: [ RUN ] CompileTimeStringJoin.Works 18: [ OK ] CompileTimeStringJoin.Works (0 ms) 18: [----------] 1 test from CompileTimeStringJoin (0 ms total) 18: 18: [----------] 3 tests from TemplateMPTest 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 18: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 18: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 18: [----------] 3 tests from TemplateMPTest (0 ms total) 18: 18: [----------] 8 tests from TextWriterTest 18: [ RUN ] TextWriterTest.WritesLines 18: [ OK ] TextWriterTest.WritesLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInParts 18: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 18: [ RUN ] TextWriterTest.WritesWrappedLines 18: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 18: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 18: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 18: [ RUN ] TextWriterTest.TracksNewlines 18: [ OK ] TextWriterTest.TracksNewlines (0 ms) 18: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 18: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 18: [ RUN ] TextWriterTest.WritesIndentedLines 18: [ OK ] TextWriterTest.WritesIndentedLines (0 ms) 18: [ RUN ] TextWriterTest.ScopedIndenterWritesIndentedLines 18: [ OK ] TextWriterTest.ScopedIndenterWritesIndentedLines (0 ms) 18: [----------] 8 tests from TextWriterTest (1 ms total) 18: 18: [----------] 4 tests from DumpingTextTest 18: [ RUN ] DumpingTextTest.LegacyIndentingWorks 18: [ OK ] DumpingTextTest.LegacyIndentingWorks (0 ms) 18: [ RUN ] DumpingTextTest.ReportsWhenNotAvailableIdentically 18: [ OK ] DumpingTextTest.ReportsWhenNotAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.QuietWhenAvailableIdentically 18: [ OK ] DumpingTextTest.QuietWhenAvailableIdentically (0 ms) 18: [ RUN ] DumpingTextTest.PrintsTitleAndSizeIdentically 18: [ OK ] DumpingTextTest.PrintsTitleAndSizeIdentically (0 ms) 18: [----------] 4 tests from DumpingTextTest (0 ms total) 18: 18: [----------] 1 test from TypeTraitsTest 18: [ RUN ] TypeTraitsTest.IsIntegralConstant 18: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 18: [----------] 1 test from TypeTraitsTest (0 ms total) 18: 18: [----------] 41 tests from RVecTest 18: [ RUN ] RVecTest.CanBeStoredInVector 18: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 18: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 18: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAsMutable_rvec 18: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Array 18: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 18: [ RUN ] RVecTest.ComparesEqual 18: [ OK ] RVecTest.ComparesEqual (0 ms) 18: [ RUN ] RVecTest.ComparesUnequal 18: [ OK ] RVecTest.ComparesUnequal (0 ms) 18: [ RUN ] RVecTest.CanAddRVecToRvec 18: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanAddAssignRVecToRvec 18: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractRVecFromRvec 18: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 18: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 18: [ RUN ] RVecTest.CanDotProductRVecByRvec 18: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanCrossProductRVecByRvec 18: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVecInplace 18: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 18: [ RUN ] RVecTest.CanScaleRVec 18: [ OK ] RVecTest.CanScaleRVec (0 ms) 18: [ RUN ] RVecTest.CanDivideRVec 18: [ OK ] RVecTest.CanDivideRVec (0 ms) 18: [ RUN ] RVecTest.CanDoUnitvFromRVec 18: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanSqLengthOfRVec 18: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanLengthOfRVec 18: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToRVec 18: [ OK ] RVecTest.CanCastToRVec (0 ms) 18: [ RUN ] RVecTest.CanCastToDVec 18: [ OK ] RVecTest.CanCastToDVec (0 ms) 18: [ RUN ] RVecTest.CanLeftScalarMultiply 18: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanRightScalarMultiply 18: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 18: [ RUN ] RVecTest.CanGetUnitvFromRVec 18: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 18: [ RUN ] RVecTest.CanGetSqLengthOfRVec 18: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanGetLengthOfRVec 18: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoCrossProductOfRVec 18: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanDoDotProductOfRVec 18: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 18: [ RUN ] RVecTest.CanScaleByVector 18: [ OK ] RVecTest.CanScaleByVector (0 ms) 18: [ RUN ] RVecTest.CanNegate 18: [ OK ] RVecTest.CanNegate (0 ms) 18: [ RUN ] RVecTest.asIVec 18: [ OK ] RVecTest.asIVec (0 ms) 18: [ RUN ] RVecTest.elementWiseMin 18: [ OK ] RVecTest.elementWiseMin (0 ms) 18: [ RUN ] RVecTest.elementWiseMax 18: [ OK ] RVecTest.elementWiseMax (0 ms) 18: [ RUN ] RVecTest.WorksAs_dvec_Reference 18: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_ivec_Reference 18: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 18: [ RUN ] RVecTest.WorksAs_rvec_Reference 18: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 18: [ RUN ] RVecTest.CopyConstructorWorks 18: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 18: [ RUN ] RVecTest.CopyAssignmentWorks 18: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.MoveConstructorWorks 18: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 18: [ RUN ] RVecTest.MoveAssignmentWorks 18: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 18: [ RUN ] RVecTest.UsableInConstexpr 18: [ OK ] RVecTest.UsableInConstexpr (0 ms) 18: [----------] 41 tests from RVecTest (0 ms total) 18: 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 18: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 18: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 18: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 18: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 18: 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 18: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 18: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 18: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 18: 18: [----------] 11 tests from WithInputPaths/PathSearchTest 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 18: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 18: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 18: [----------] 11 tests from WithInputPaths/PathSearchTest (1 ms total) 18: 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 18: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 18: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 18: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 18: 18: [----------] 24 tests from Works/DumpingVectorsTest 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpIntBlocks/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpFloatIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpDoubleIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRealIdentically/3 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/0 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/1 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/2 (0 ms) 18: [ RUN ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 18: [ OK ] Works/DumpingVectorsTest.CanDumpRvecIdentically/3 (0 ms) 18: [----------] 24 tests from Works/DumpingVectorsTest (3 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 495 tests from 68 test suites ran. (28 ms total) 18: [ PASSED ] 485 tests. 18: [ SKIPPED ] 10 tests, listed below: 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 18: [ SKIPPED ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 18: [ SKIPPED ] MpiComm.ConstructorThrowsOnNull 18: [ SKIPPED ] MpiComm.CopyConstructorWorks 18: [ SKIPPED ] MpiComm.AssigmentWorks 18: [ SKIPPED ] MpiComm.AssigmentWorksForSelf 18: [ SKIPPED ] MpiComm.MoveAssigmentWorks 18: [ SKIPPED ] MpiComm.MoveAssigmentWorksForSelf 18: 18: YOU HAVE 1 DISABLED TEST 18: 18/103 Test #18: UtilityUnitTests .......................... Passed 0.08 sec test 19 Start 19: MpiCommTests 19: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mpicomm-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MpiCommTests.xml" 19: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests 19: Test timeout computed to be: 30 19: [==========] Running 12 tests from 1 test suite. 19: [----------] Global test environment set-up. 19: [----------] 12 tests from MpiComm 19: [ RUN ] MpiComm.SingleRankNoComm 19: [ OK ] MpiComm.SingleRankNoComm (0 ms) 19: [ RUN ] MpiComm.CommWorld 19: [ OK ] MpiComm.CommWorld (11 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks1Node 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks1Node (21 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks4Nodes (0 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2EqualNodes (0 ms) 19: [ RUN ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes 19: [ OK ] MpiComm.CreatesHierarchicalReducer4Ranks2UnequalNodes (6 ms) 19: [ RUN ] MpiComm.ConstructorThrowsOnNull 19: [ OK ] MpiComm.ConstructorThrowsOnNull (1 ms) 19: [ RUN ] MpiComm.CopyConstructorWorks 19: [ OK ] MpiComm.CopyConstructorWorks (0 ms) 19: [ RUN ] MpiComm.AssigmentWorks 19: [ OK ] MpiComm.AssigmentWorks (0 ms) 19: [ RUN ] MpiComm.AssigmentWorksForSelf 19: [ OK ] MpiComm.AssigmentWorksForSelf (0 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorks 19: [ OK ] MpiComm.MoveAssigmentWorks (0 ms) 19: [ RUN ] MpiComm.MoveAssigmentWorksForSelf 19: [ OK ] MpiComm.MoveAssigmentWorksForSelf (0 ms) 19: [----------] 12 tests from MpiComm (46 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 12 tests from 1 test suite ran. (47 ms total) 19: [ PASSED ] 12 tests. 19/103 Test #19: MpiCommTests .............................. Passed 0.07 sec test 20 Start 20: UtilityMpiUnitTests 20: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 20: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/utility/tests 20: Test timeout computed to be: 30 20: [==========] Running 7 tests from 2 test suites. 20: [----------] Global test environment set-up. 20: [----------] 5 tests from CoordinateExceptionHandlingTest 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueNeverThrow (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithReturnValueAlwaysReturnThatValue (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowAlwaysThrow (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly 20: [ OK ] CoordinateExceptionHandlingTest.CallablesWithoutReturnValueThatThrowsOnOneRankAlwaysThrowCorrectly (0 ms) 20: [ RUN ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow 20: [ OK ] CoordinateExceptionHandlingTest.NulledCallablesAlwaysThrow (0 ms) 20: [----------] 5 tests from CoordinateExceptionHandlingTest (2 ms total) 20: 20: [----------] 2 tests from PhysicalNodeCommunicatorTest 20: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 20: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 20: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 20: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 20: [----------] 2 tests from PhysicalNodeCommunicatorTest (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 7 tests from 2 test suites ran. (3 ms total) 20: [ PASSED ] 7 tests. 20/103 Test #20: UtilityMpiUnitTests ....................... Passed 0.03 sec test 21 Start 21: AwhTest 21: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/AwhTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/awh/tests 21: Test timeout computed to be: 30 21: [==========] Running 27 tests from 10 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from SerializationTest 21: [ RUN ] SerializationTest.CanSerializeDimParams 21: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 21: [ RUN ] SerializationTest.CanSerializeBiasParams 21: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 21: [ RUN ] SerializationTest.CanSerializeAwhParams 21: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 21: [----------] 3 tests from SerializationTest (0 ms total) 21: 21: [----------] 1 test from BiasTest 21: [ RUN ] BiasTest.DetectsCovering 21: [ OK ] BiasTest.DetectsCovering (2 ms) 21: [----------] 1 test from BiasTest (2 ms total) 21: 21: [----------] 1 test from biasGridTest 21: [ RUN ] biasGridTest.neighborhood 21: [ OK ] biasGridTest.neighborhood (2 ms) 21: [----------] 1 test from biasGridTest (2 ms total) 21: 21: [----------] 2 tests from BiasSharingTest 21: [ RUN ] BiasSharingTest.SharingWorks 21: [ OK ] BiasSharingTest.SharingWorks (2 ms) 21: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 21: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (12 ms) 21: [----------] 2 tests from BiasSharingTest (15 ms total) 21: 21: [----------] 2 tests from BiasFepLambdaStateTest 21: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 21: [ OK ] BiasFepLambdaStateTest.DetectsCovering (7 ms) 21: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 21: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 21: [----------] 2 tests from BiasFepLambdaStateTest (8 ms total) 21: 21: [----------] 8 tests from WithParameters/BiasTest 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (1 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (1 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 21: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 21: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 21: [----------] 8 tests from WithParameters/BiasTest (8 ms total) 21: 21: [----------] 2 tests from WithParameters/BiasStateTest 21: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 21: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms) 21: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 21: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 21: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 21: 21: [----------] 1 test from WithParameters/UserInputTest 21: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 21: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 21: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 21: 21: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 21: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 21: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (14 ms) 21: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 21: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (15 ms) 21: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 21: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (15 ms) 21: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 21: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (15 ms) 21: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (63 ms total) 21: 21: [----------] 3 tests from WithParameters/FrictionMetricTest 21: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 21: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 21: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 21: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (2 ms) 21: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 21: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (44 ms) 21: [----------] 3 tests from WithParameters/FrictionMetricTest (53 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 27 tests from 10 test suites ran. (158 ms total) 21: [ PASSED ] 27 tests. 21/103 Test #21: AwhTest ................................... Passed 0.19 sec test 22 Start 22: DensityFittingAppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 22: Test timeout computed to be: 30 22: [==========] Running 18 tests from 4 test suites. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from DensityFittingTest 22: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 22: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 22: [ RUN ] DensityFittingTest.SingleAtom 22: [ OK ] DensityFittingTest.SingleAtom (2 ms) 22: [----------] 2 tests from DensityFittingTest (2 ms total) 22: 22: [----------] 7 tests from DensityFittingAmplitudeLookupTest 22: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 22: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 22: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 22: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 22: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 22: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 22: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 22: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 22: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 22: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 22: 22: [----------] 1 test from DensityFittingForceProviderState 22: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 22: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 22: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 22: 22: [----------] 8 tests from DensityFittingOptionsTest 22: [ RUN ] DensityFittingOptionsTest.DefaultParameters 22: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 22: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 22: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 22: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 22: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 22: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 22: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 22: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 22: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 22: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 22: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 22: [ RUN ] DensityFittingOptionsTest.KvtToInternal 22: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 22: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 22: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 22: [----------] 8 tests from DensityFittingOptionsTest (1 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 18 tests from 4 test suites ran. (4 ms total) 22: [ PASSED ] 18 tests. 22/103 Test #22: DensityFittingAppliedForcesUnitTest ....... Passed 0.03 sec test 23 Start 23: QMMMAppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests 23: Test timeout computed to be: 30 23: [==========] Running 28 tests from 7 test suites. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from QMMMInputGeneratorTest 23: [ RUN ] QMMMInputGeneratorTest.CanConstruct 23: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 23: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 23: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 23: [----------] 2 tests from QMMMInputGeneratorTest (1 ms total) 23: 23: [----------] 6 tests from QMMMTopologyPreprocessorTest 23: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: Setting the LD random seed to -1212810441 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (11 ms) 23: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: Setting the LD random seed to -3579555 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (10 ms) 23: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 21.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: 23: WARNING 1 [file unknown]: 23: Total charge of your embedded system differs from classical system! 23: Consider manually spreading -0.41000 charge over MM atoms near to the 23: embedded region 23: 23: 23: Setting the LD random seed to -1656304266 23: 23: Generated 10 of the 10 non-bonded parameter combinations 23: 23: Generated 10 of the 10 1-4 parameter combinations 23: 23: Excluding 2 bonded neighbours molecule type 'SOL' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 23: Analysing residue names: 23: There are: 4 Water residues 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (9 ms) 23: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: Number of degrees of freedom in T-Coupling group rest is 63.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 129.093 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: 23: WARNING 1 [file unknown]: 23: Total charge of your embedded system differs from classical system! 23: Consider manually spreading 0.11440 charge over MM atoms near to the 23: embedded region 23: 23: 23: Setting the LD random seed to 1983852399 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (26 ms) 23: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Generating 1-4 interactions: fudge = 0.5 23: 23: NOTE 2 [file unknown]: 23: You are using constraints on all bonds, whereas the forcefield has been 23: parametrized only with constraints involving hydrogen atoms. We suggest 23: using constraints = h-bonds instead, this will also improve performance. 23: 23: 23: NOTE 3 [file unknown]: 23: For energy conservation with LINCS, lincs_iter should be 2 or larger. 23: 23: 23: Number of degrees of freedom in T-Coupling group rest is 42.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 23: NVE simulation: will use the initial temperature of 193.640 K for 23: determining the Verlet buffer size 23: 23: 23: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 5 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: 23: WARNING 1 [file unknown]: 23: Total charge of your embedded system differs from classical system! 23: Consider manually spreading 0.11440 charge over MM atoms near to the 23: embedded region 23: 23: 23: 23: WARNING 2 [file unknown]: 23: Your embedded subsystem has a lot of constrained bonds. They probably 23: have been generated automatically. That could produce artifacts in the 23: simulation. Consider constraints = none in the mdp file. 23: 23: 23: Setting the LD random seed to 1048574935 23: 23: Generated 2145 of the 2145 non-bonded parameter combinations 23: 23: Generated 2145 of the 2145 1-4 parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 23: 23: turning all bonds into constraints... 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 23: Analysing residue names: 23: There are: 3 Protein residues 23: Analysing Protein... 23: 23: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 23: 23: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 23: 23: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 23: 23: Note that mdrun will redetermine rlist based on the actual pair-list setup 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (29 ms) 23: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 23: 23: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 23: For a correct single-point energy evaluation with nsteps = 0, use 23: continuation = yes to avoid constraining the input coordinates. 23: 23: Number of degrees of freedom in T-Coupling group rest is 45.00 23: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 23: 23: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 23: NVE simulation with an initial temperature of zero: will use a Verlet 23: buffer of 10%. Check your energy drift! 23: 23: 23: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 23: You are using a plain Coulomb cut-off, which might produce artifacts. 23: You might want to consider using PME electrostatics. 23: 23: 23: 23: There were 3 NOTEs 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 23: Setting the LD random seed to -1932044564 23: 23: Generated 3 of the 6 non-bonded parameter combinations 23: 23: Excluding 3 bonded neighbours molecule type 'VSTEST' 23: 23: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 23: 23: Cleaning up constraints and constant bonded interactions with virtual sites 23: Analysing residue names: 23: There are: 1 Other residues 23: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 23: 23: This run will generate roughly 0 Mb of data 23: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (11 ms) 23: [----------] 6 tests from QMMMTopologyPreprocessorTest (99 ms total) 23: 23: [----------] 9 tests from QMMMOptionsTest 23: [ RUN ] QMMMOptionsTest.DefaultParameters 23: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 23: [ RUN ] QMMMOptionsTest.OptionSetsActive 23: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 23: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 23: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 23: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 23: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 23: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 23: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 23: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 23: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 23: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 23: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 23: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 23: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 23: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 23: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 23: [----------] 9 tests from QMMMOptionsTest (3 ms total) 23: 23: [----------] 3 tests from QMMMForceProviderStateTest 23: [ RUN ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint 23: [ OK ] QMMMForceProviderStateTest.WritesTranslationVectorToCheckpoint (0 ms) 23: [ RUN ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent 23: [ OK ] QMMMForceProviderStateTest.ReadsTranslationVectorWhenPresent (0 ms) 23: [ RUN ] QMMMForceProviderStateTest.MissingStateWhenNoData 23: [ OK ] QMMMForceProviderStateTest.MissingStateWhenNoData (0 ms) 23: [----------] 3 tests from QMMMForceProviderStateTest (0 ms total) 23: 23: [----------] 1 test from QMMMForceProviderTest 23: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 23: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 23: [----------] 1 test from QMMMForceProviderTest (0 ms total) 23: 23: [----------] 1 test from QMMMTest 23: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 23: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 23: [----------] 1 test from QMMMTest (0 ms total) 23: 23: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBENoLink (0 ms) 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0NoLink (0 ms) 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersPBE0D3NoLink (0 ms) 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersCAMB3LYPNoLink (0 ms) 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XNoLink (0 ms) 23: [ RUN ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink 23: [ OK ] QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest.TwoWatersNoLink/TwoWatersWB97XD3NoLink (0 ms) 23: [----------] 6 tests from QMMMInputGeneratorTest/QMMMInputGeneratorMethodTest (3 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 28 tests from 7 test suites ran. (108 ms total) 23: [ PASSED ] 28 tests. 23/103 Test #23: QMMMAppliedForcesUnitTest ................. Passed 0.14 sec test 24 Start 24: ColvarsAppliedForcesUnitTest 24: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests 24: Test timeout computed to be: 30 24: [==========] Running 16 tests from 4 test suites. 24: [----------] Global test environment set-up. 24: [----------] 1 test from ColvarsTest 24: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 24: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 24: [----------] 1 test from ColvarsTest (0 ms total) 24: 24: [----------] 6 tests from ColvarsOptionsTest 24: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 24: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 24: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 24: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 24: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 24: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (1 ms) 24: [ RUN ] ColvarsOptionsTest.OptionSetsActive 24: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 24: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Setting the LD random seed to 964656639 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (18 ms) 24: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 24: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 24: [----------] 6 tests from ColvarsOptionsTest (21 ms total) 24: 24: [----------] 4 tests from ColvarsPreProcessorTest 24: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Setting the LD random seed to -1344344321 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (9 ms) 24: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Setting the LD random seed to -143671297 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (12 ms) 24: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Setting the LD random seed to -545 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (12 ms) 24: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Setting the LD random seed to -1086485505 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (13 ms) 24: [----------] 4 tests from ColvarsPreProcessorTest (48 ms total) 24: 24: [----------] 5 tests from ColvarsForceProviderTest 24: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 24: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (1 ms) 24: [ RUN ] ColvarsForceProviderTest.SimpleInputs 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Setting the LD random seed to -537133569 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsForceProviderTest.SimpleInputs (11 ms) 24: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Setting the LD random seed to -67214338 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (10 ms) 24: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 21.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 24: NVE simulation with an initial temperature of zero: will use a Verlet 24: buffer of 10%. Check your energy drift! 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Setting the LD random seed to -2114057 24: 24: Generated 10 of the 10 non-bonded parameter combinations 24: 24: Generated 10 of the 10 1-4 parameter combinations 24: 24: Excluding 2 bonded neighbours molecule type 'SOL' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 24: Analysing residue names: 24: There are: 4 Water residues 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsForceProviderTest.CalculateForces4water (12 ms) 24: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 24: 24: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 24: For a correct single-point energy evaluation with nsteps = 0, use 24: continuation = yes to avoid constraining the input coordinates. 24: 24: Generating 1-4 interactions: fudge = 0.5 24: Number of degrees of freedom in T-Coupling group rest is 66.00 24: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 24: 24: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 24: NVE simulation: will use the initial temperature of 300.368 K for 24: determining the Verlet buffer size 24: 24: 24: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 24: You are using a plain Coulomb cut-off, which might produce artifacts. 24: You might want to consider using PME electrostatics. 24: 24: 24: 24: There were 3 NOTEs 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 24: Setting the LD random seed to -273228289 24: 24: Generated 2211 of the 2211 non-bonded parameter combinations 24: 24: Generated 2211 of the 2211 1-4 parameter combinations 24: 24: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 24: 24: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 24: Analysing residue names: 24: There are: 2 Protein residues 24: Analysing Protein... 24: 24: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 24: 24: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 24: 24: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 24: 24: Note that mdrun will redetermine rlist based on the actual pair-list setup 24: 24: This run will generate roughly 0 Mb of data 24: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (34 ms) 24: [----------] 5 tests from ColvarsForceProviderTest (70 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 16 tests from 4 test suites ran. (140 ms total) 24: [ PASSED ] 16 tests. 24/103 Test #24: ColvarsAppliedForcesUnitTest .............. Passed 0.17 sec test 25 Start 25: PlumedAppliedForcesUnitTests 25: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/plumed_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/PlumedAppliedForcesUnitTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests 25: Test timeout computed to be: 30 25: [==========] Running 8 tests from 1 test suite. 25: [----------] Global test environment set-up. 25: [----------] 8 tests from PlumedOptionsTest 25: [ RUN ] PlumedOptionsTest.defaultConstructor 25: [ OK ] PlumedOptionsTest.defaultConstructor (0 ms) 25: [ RUN ] PlumedOptionsTest.setTimeStep 25: [ OK ] PlumedOptionsTest.setTimeStep (0 ms) 25: [ RUN ] PlumedOptionsTest.setStartingBehavior 25: [ OK ] PlumedOptionsTest.setStartingBehavior (1 ms) 25: [ RUN ] PlumedOptionsTest.setPlumedFile 25: [ OK ] PlumedOptionsTest.setPlumedFile (0 ms) 25: [ RUN ] PlumedOptionsTest.setPlumedFileNotSet 25: [ OK ] PlumedOptionsTest.setPlumedFileNotSet (0 ms) 25: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_data 25: [ OK ] PlumedOptionsTest.setEnsembleTemperature_data (0 ms) 25: [ RUN ] PlumedOptionsTest.setEnsembleTemperature_notConstant 25: [ OK ] PlumedOptionsTest.setEnsembleTemperature_notConstant (0 ms) 25: [ RUN ] PlumedOptionsTest.setTopology 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 21.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: 25: NOTE 2 [file angles1.top, line 72]: 25: In moleculetype 'butane' 4 atoms are not bound by a potential or 25: constraint to any other atom in the same moleculetype. Although 25: technically this might not cause issues in a simulation, this often means 25: that the user forgot to add a bond/potential/constraint or put multiple 25: molecules in the same moleculetype definition by mistake. Run with -v to 25: get information for each atom. 25: 25: Number of degrees of freedom in T-Coupling group rest is 9.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.mdp]: 25: NVE simulation: will use the initial temperature of 238.919 K for 25: determining the Verlet buffer size 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_angles1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Number of degrees of freedom in T-Coupling group rest is 17493.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.mdp]: 25: NVE simulation: will use the initial temperature of 67.983 K for 25: determining the Verlet buffer size 25: 25: 25: There were 2 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon5832.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Number of degrees of freedom in T-Coupling group rest is 9.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: There were 2 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_argon4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Number of degrees of freedom in T-Coupling group rest is 9.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 25: NVE simulation with an initial temperature of zero: will use a Verlet 25: buffer of 10%. Check your energy drift! 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_dipoles.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: 25: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 25: For a correct single-point energy evaluation with nsteps = 0, use 25: continuation = yes to avoid constraining the input coordinates. 25: 25: Generating 1-4 interactions: fudge = 0.5 25: Number of degrees of freedom in T-Coupling group rest is 18.00 25: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 25: 25: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 25: NVE simulation: will use the initial temperature of 135.187 K for 25: determining the Verlet buffer size 25: 25: 25: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.mdp]: 25: You are using a plain Coulomb cut-off, which might produce artifacts. 25: You might want to consider using PME electrostatics. 25: 25: 25: 25: There were 3 NOTEs 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests/Testing/Temporary/PlumedOptionsTest_setTopology_spc_and_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 25: Setting the LD random seed to -821762 25: 25: Generated 10 of the 10 non-bonded parameter combinations 25: 25: Generated 10 of the 10 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Water residues 25: 25: This run will generate roughly 0 Mb of data 25: Setting the LD random seed to -276846686 25: 25: Generated 3 of the 3 non-bonded parameter combinations 25: 25: Excluding 3 bonded neighbours molecule type 'butane' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/angles1.gro' 25: Analysing residue names: 25: There are: 1 Other residues 25: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 238.919 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: Setting the LD random seed to 1585166845 25: 25: Generated 1 of the 1 non-bonded parameter combinations 25: 25: Excluding 1 bonded neighbours molecule type 'Argon' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon5832.gro' 25: Analysing residue names: 25: There are: 5832 Other residues 25: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 67.9831 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.001 nm, buffer size 0.001 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: Setting the LD random seed to -1207959569 25: 25: Generated 1 of the 1 non-bonded parameter combinations 25: 25: Excluding 1 bonded neighbours molecule type 'ArgonA' 25: 25: Excluding 1 bonded neighbours molecule type 'ArgonB' 25: 25: Excluding 1 bonded neighbours molecule type 'ArgonC' 25: 25: Excluding 1 bonded neighbours molecule type 'ArgonD' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 25: Analysing residue names: 25: There are: 4 Other residues 25: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 25: 25: This run will generate roughly 0 Mb of data 25: Setting the LD random seed to -76161257 25: 25: Generated 1 of the 1 non-bonded parameter combinations 25: 25: Excluding 1 bonded neighbours molecule type 'Dipole' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 25: Analysing residue names: 25: There are: 2 Other residues 25: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 25: 25: This run will generate roughly 0 Mb of data 25: Setting the LD random seed to -247529514 25: 25: Generated 331705 of the 331705 non-bonded parameter combinations 25: 25: Generated 331705 of the 331705 1-4 parameter combinations 25: 25: Excluding 2 bonded neighbours molecule type 'SOL' 25: 25: Excluding 3 bonded neighbours molecule type 'methane' 25: 25: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc_and_methane.gro' 25: Analysing residue names: 25: There are: 1 Water residues 25: There are: 1 Other residues 25: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 25: 25: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 135.187 K 25: 25: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 25: 25: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 25: 25: Note that mdrun will redetermine rlist based on the actual pair-list setup 25: 25: This run will generate roughly 0 Mb of data 25: [ OK ] PlumedOptionsTest.setTopology (1083 ms) 25: [----------] 8 tests from PlumedOptionsTest (1087 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 8 tests from 1 test suite ran. (1087 ms total) 25: [ PASSED ] 8 tests. 25/103 Test #25: PlumedAppliedForcesUnitTests .............. Passed 1.12 sec test 26 Start 26: PlumedMDTests 26: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/plumed_md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/PlumedMDTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/plumed/tests 26: Test timeout computed to be: 600 26: [==========] Running 2 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 2 tests from SimplePlumedMD/PlumedRun 26: [ RUN ] SimplePlumedMD/PlumedRun.PlumedSees/0 26: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 26: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 26: 26: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 (0 ms) 26: [ RUN ] SimplePlumedMD/PlumedRun.PlumedDoes/0 26: ./src/gromacs/applied_forces/plumed/tests/plumed_md_test.cpp:92: Skipped 26: The GMX_TEST_PLUMED_KERNEL_IS_AVAILABLE environment variable is not set, and the PLUMED kernel was not found. 26: 26: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 (0 ms) 26: [----------] 2 tests from SimplePlumedMD/PlumedRun (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 2 tests from 1 test suite ran. (16 ms total) 26: [ PASSED ] 0 tests. 26: [ SKIPPED ] 2 tests, listed below: 26: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedSees/0 26: [ SKIPPED ] SimplePlumedMD/PlumedRun.PlumedDoes/0 26/103 Test #26: PlumedMDTests ............................. Passed 0.04 sec test 27 Start 27: NNPotAppliedForcesUnitTest 27: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nnpot_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/NNPotAppliedForcesUnitTest.xml" 27: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests 27: Test timeout computed to be: 30 27: [==========] Running 17 tests from 4 test suites. 27: [----------] Global test environment set-up. 27: [----------] 1 test from NNPotTest 27: [ RUN ] NNPotTest.ForceProviderLackingInputThrows 27: [ OK ] NNPotTest.ForceProviderLackingInputThrows (0 ms) 27: [----------] 1 test from NNPotTest (0 ms total) 27: 27: [----------] 5 tests from NNPotOptionsTest 27: [ RUN ] NNPotOptionsTest.DefaultParameters 27: [ OK ] NNPotOptionsTest.DefaultParameters (36 ms) 27: [ RUN ] NNPotOptionsTest.OptionSetsActive 27: [ OK ] NNPotOptionsTest.OptionSetsActive (0 ms) 27: [ RUN ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive 27: [ OK ] NNPotOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 27: [ RUN ] NNPotOptionsTest.OutputDefaultValuesWhenActive 27: [ OK ] NNPotOptionsTest.OutputDefaultValuesWhenActive (0 ms) 27: [ RUN ] NNPotOptionsTest.InternalsToKvtAndBack 27: [ OK ] NNPotOptionsTest.InternalsToKvtAndBack (0 ms) 27: [----------] 5 tests from NNPotOptionsTest (37 ms total) 27: 27: [----------] 1 test from NNPotForceProviderTest 27: [ RUN ] NNPotForceProviderTest.CanConstruct 27: [ OK ] NNPotForceProviderTest.CanConstruct (0 ms) 27: [----------] 1 test from NNPotForceProviderTest (0 ms total) 27: 27: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 21.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_0_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Setting the LD random seed to -948013185 27: 27: Generated 10 of the 10 non-bonded parameter combinations 27: 27: Generated 10 of the 10 1-4 parameter combinations 27: 27: Excluding 2 bonded neighbours molecule type 'SOL' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 27: Analysing residue names: 27: There are: 4 Water residues 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/0 (10 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 21.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersFirstInNNPRegion_1_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Setting the LD random seed to 2121201643 27: 27: Generated 10 of the 10 non-bonded parameter combinations 27: 27: Generated 10 of the 10 1-4 parameter combinations 27: 27: Excluding 2 bonded neighbours molecule type 'SOL' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 27: Analysing residue names: 27: There are: 4 Water residues 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersFirstInNNPRegion/1 (10 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 21.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_0_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Setting the LD random seed to -409079180 27: 27: Generated 10 of the 10 non-bonded parameter combinations 27: 27: Generated 10 of the 10 1-4 parameter combinations 27: 27: Excluding 2 bonded neighbours molecule type 'SOL' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 27: Analysing residue names: 27: There are: 4 Water residues 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/0 (9 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 21.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_FourWatersSecondAndFourthInNNPRegion_1_4water.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Setting the LD random seed to -1083322401 27: 27: Generated 10 of the 10 non-bonded parameter combinations 27: 27: Generated 10 of the 10 1-4 parameter combinations 27: 27: Excluding 2 bonded neighbours molecule type 'SOL' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 27: Analysing residue names: 27: There are: 4 Water residues 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.FourWatersSecondAndFourthInNNPRegion/1 (10 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 63.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 27: NVE simulation: will use the initial temperature of 129.093 K for 27: determining the Verlet buffer size 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_0_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Setting the LD random seed to -205594753 27: 27: Generated 2145 of the 2145 non-bonded parameter combinations 27: 27: Generated 2145 of the 2145 1-4 parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 27: Analysing residue names: 27: There are: 3 Protein residues 27: Analysing Protein... 27: 27: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 27: 27: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 27: 27: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 27: 27: Note that mdrun will redetermine rlist based on the actual pair-list setup 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/0 (26 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: Number of degrees of freedom in T-Coupling group rest is 63.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 27: NVE simulation: will use the initial temperature of 129.093 K for 27: determining the Verlet buffer size 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsNoConstraints_1_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: 27: WARNING 1 [file unknown]: 27: Total charge of your embedded system differs from classical system! 27: Consider manually spreading 0.11440 charge over MM atoms near to the 27: embedded region 27: 27: 27: Setting the LD random seed to -1130370565 27: 27: Generated 2145 of the 2145 non-bonded parameter combinations 27: 27: Generated 2145 of the 2145 1-4 parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 27: Analysing residue names: 27: There are: 3 Protein residues 27: Analysing Protein... 27: 27: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 27: 27: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 27: 27: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 27: 27: Note that mdrun will redetermine rlist based on the actual pair-list setup 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsNoConstraints/1 (27 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: 27: NOTE 2 [file unknown]: 27: You are using constraints on all bonds, whereas the forcefield has been 27: parametrized only with constraints involving hydrogen atoms. We suggest 27: using constraints = h-bonds instead, this will also improve performance. 27: 27: 27: NOTE 3 [file unknown]: 27: For energy conservation with LINCS, lincs_iter should be 2 or larger. 27: 27: 27: Number of degrees of freedom in T-Coupling group rest is 42.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 27: NVE simulation: will use the initial temperature of 193.640 K for 27: determining the Verlet buffer size 27: 27: 27: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 5 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_0_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: 27: WARNING 1 [file unknown]: 27: Your embedded subsystem has a lot of constrained bonds. They probably 27: have been generated automatically. That could produce artifacts in the 27: simulation. Consider constraints = none in the mdp file. 27: 27: 27: Setting the LD random seed to -335675535 27: 27: Generated 2145 of the 2145 non-bonded parameter combinations 27: 27: Generated 2145 of the 2145 1-4 parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 27: 27: turning all bonds into constraints... 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 27: Analysing residue names: 27: There are: 3 Protein residues 27: Analysing Protein... 27: 27: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 27: 27: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 27: 27: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 27: 27: Note that mdrun will redetermine rlist based on the actual pair-list setup 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/0 (29 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Generating 1-4 interactions: fudge = 0.5 27: 27: NOTE 2 [file unknown]: 27: You are using constraints on all bonds, whereas the forcefield has been 27: parametrized only with constraints involving hydrogen atoms. We suggest 27: using constraints = h-bonds instead, this will also improve performance. 27: 27: 27: NOTE 3 [file unknown]: 27: For energy conservation with LINCS, lincs_iter should be 2 or larger. 27: 27: 27: Number of degrees of freedom in T-Coupling group rest is 42.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 27: NVE simulation: will use the initial temperature of 193.640 K for 27: determining the Verlet buffer size 27: 27: 27: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 5 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_AlanineDipeptideWithLinkAtomsWithConstraints_1_alanine_vacuo.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: 27: WARNING 1 [file unknown]: 27: Total charge of your embedded system differs from classical system! 27: Consider manually spreading 0.11440 charge over MM atoms near to the 27: embedded region 27: 27: 27: 27: WARNING 2 [file unknown]: 27: Your embedded subsystem has a lot of constrained bonds. They probably 27: have been generated automatically. That could produce artifacts in the 27: simulation. Consider constraints = none in the mdp file. 27: 27: 27: Setting the LD random seed to 1514864511 27: 27: Generated 2145 of the 2145 non-bonded parameter combinations 27: 27: Generated 2145 of the 2145 1-4 parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 27: 27: turning all bonds into constraints... 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 27: Analysing residue names: 27: There are: 3 Protein residues 27: Analysing Protein... 27: 27: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 27: 27: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 27: 27: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 27: 27: Note that mdrun will redetermine rlist based on the actual pair-list setup 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.AlanineDipeptideWithLinkAtomsWithConstraints/1 (29 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Number of degrees of freedom in T-Coupling group rest is 45.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_0_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Setting the LD random seed to -143149297 27: 27: Generated 3 of the 6 non-bonded parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'VSTEST' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 27: 27: Cleaning up constraints and constant bonded interactions with virtual sites 27: Analysing residue names: 27: There are: 1 Other residues 27: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/0 (11 ms) 27: [ RUN ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 27: 27: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 27: For a correct single-point energy evaluation with nsteps = 0, use 27: continuation = yes to avoid constraining the input coordinates. 27: 27: Number of degrees of freedom in T-Coupling group rest is 45.00 27: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 27: 27: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 27: NVE simulation with an initial temperature of zero: will use a Verlet 27: buffer of 10%. Check your energy drift! 27: 27: 27: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.mdp]: 27: You are using a plain Coulomb cut-off, which might produce artifacts. 27: You might want to consider using PME electrostatics. 27: 27: 27: 27: There were 3 NOTEs 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/nnpot/tests/Testing/Temporary/NNPotTopologyPreprocessorTests_NNPotTopologyPreprocessorTest_RemovingChargeOnVSites_1_vsite_test.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 27: Setting the LD random seed to -436733962 27: 27: Generated 3 of the 6 non-bonded parameter combinations 27: 27: Excluding 3 bonded neighbours molecule type 'VSTEST' 27: 27: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 27: 27: Cleaning up constraints and constant bonded interactions with virtual sites 27: Analysing residue names: 27: There are: 1 Other residues 27: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 27: 27: This run will generate roughly 0 Mb of data 27: [ OK ] NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest.RemovingChargeOnVSites/1 (11 ms) 27: [----------] 10 tests from NNPotTopologyPreprocessorTests/NNPotTopologyPreprocessorTest (176 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 17 tests from 4 test suites ran. (215 ms total) 27: [ PASSED ] 17 tests. 27/103 Test #27: NNPotAppliedForcesUnitTest ................ Passed 0.26 sec test 28 Start 28: AppliedForcesUnitTest 28: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 28: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/applied_forces/tests 28: Test timeout computed to be: 30 28: [==========] Running 3 tests from 1 test suite. 28: [----------] Global test environment set-up. 28: [----------] 3 tests from ElectricFieldTest 28: [ RUN ] ElectricFieldTest.Static 28: [ OK ] ElectricFieldTest.Static (0 ms) 28: [ RUN ] ElectricFieldTest.Oscillating 28: [ OK ] ElectricFieldTest.Oscillating (0 ms) 28: [ RUN ] ElectricFieldTest.Pulsed 28: [ OK ] ElectricFieldTest.Pulsed (0 ms) 28: [----------] 3 tests from ElectricFieldTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 3 tests from 1 test suite ran. (0 ms total) 28: [ PASSED ] 3 tests. 28/103 Test #28: AppliedForcesUnitTest ..................... Passed 0.02 sec test 29 Start 29: ListedForcesTest 29: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 29: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/listed_forces/tests 29: Test timeout computed to be: 30 29: [==========] Running 132 tests from 9 test suites. 29: [----------] Global test environment set-up. 29: [----------] 24 tests from Bond/ListedForcesTest 29: [ RUN ] Bond/ListedForcesTest.Ifunc/0 29: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/1 29: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/2 29: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/3 29: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/4 29: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/5 29: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/6 29: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/7 29: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/8 29: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/9 29: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/10 29: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/11 29: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/12 29: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/13 29: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/14 29: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/15 29: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/16 29: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/17 29: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/18 29: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/19 29: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/20 29: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/21 29: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/22 29: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 29: [ RUN ] Bond/ListedForcesTest.Ifunc/23 29: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 29: [----------] 24 tests from Bond/ListedForcesTest (14 ms total) 29: 29: [----------] 33 tests from Angle/ListedForcesTest 29: [ RUN ] Angle/ListedForcesTest.Ifunc/0 29: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/1 29: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/2 29: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/3 29: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/4 29: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/5 29: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/6 29: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/7 29: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/8 29: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/9 29: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/10 29: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/11 29: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/12 29: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/13 29: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/14 29: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/15 29: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/16 29: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/17 29: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/18 29: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/19 29: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/20 29: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/21 29: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/22 29: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/23 29: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/24 29: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/25 29: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/26 29: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/27 29: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/28 29: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/29 29: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/30 29: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/31 29: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 29: [ RUN ] Angle/ListedForcesTest.Ifunc/32 29: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 29: [----------] 33 tests from Angle/ListedForcesTest (16 ms total) 29: 29: [----------] 18 tests from Dihedral/ListedForcesTest 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 29: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 29: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 29: [----------] 18 tests from Dihedral/ListedForcesTest (9 ms total) 29: 29: [----------] 12 tests from Polarize/ListedForcesTest 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 29: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 29: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 29: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 29: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 29: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 29: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 29: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 29: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 29: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 29: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 29: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 29: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 29: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 29: [----------] 12 tests from Polarize/ListedForcesTest (5 ms total) 29: 29: [----------] 18 tests from Restraints/ListedForcesTest 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 29: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 29: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 29: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 29: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 29: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 29: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 29: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 29: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 29: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 29: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 29: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 29: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 29: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 29: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 29: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 29: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 29: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 29: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 29: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 29: [----------] 18 tests from Restraints/ListedForcesTest (10 ms total) 29: 29: [----------] 3 tests from BondZeroLength/ListedForcesTest 29: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 29: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 29: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 29: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 29: [----------] 3 tests from BondZeroLength/ListedForcesTest (1 ms total) 29: 29: [----------] 3 tests from AngleZero/ListedForcesTest 29: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 29: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 29: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 29: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 29: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 29: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 29: [----------] 3 tests from AngleZero/ListedForcesTest (1 ms total) 29: 29: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 29: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 29: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 29: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (6 ms total) 29: 29: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 29: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 29: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 29: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (4 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 132 tests from 9 test suites ran. (70 ms total) 29: [ PASSED ] 132 tests. 29/103 Test #29: ListedForcesTest .......................... Passed 0.11 sec test 30 Start 30: NbnxmTests 30: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nbnxm-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/NbnxmTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests 30: Test timeout computed to be: 30 30: [==========] Running 529 tests from 4 test suites. 30: [----------] Global test environment set-up. 30: [----------] 19 tests from KernelSetupTest 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 30: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 30: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 30: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 30: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 30: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 30: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 30: [ RUN ] KernelSetupTest.getCoulombKernelTypeNone 30: [ OK ] KernelSetupTest.getCoulombKernelTypeNone (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 30: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 30: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 30: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 30: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 30: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 30: [----------] 19 tests from KernelSetupTest (0 ms total) 30: 30: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest 30: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 30: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 30: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 30: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 30: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 30: 30: [----------] 504 tests from Combinations/NbnxmKernelTest 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombNone (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwForceSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (5 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:532: Skipped 30: Analytical Ewald is not implemented for the plain-C kernel, skip this test 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwForceSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (10 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (11 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (8 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (6 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ OK ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (7 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:551: Skipped 30: Reference kernels that do not compute Coulomb interactions are available only with an FMM build configuration 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:539: Skipped 30: There are no combination rule versions of the plain-C kernel 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:544: Skipped 30: Cannot test or generate data for FMM kernels because FMM is not yet supported in GROMACS for short-range coulomb interactions 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:518: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [ RUN ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: ./src/gromacs/nbnxm/tests/kernel_test.cpp:524: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom (0 ms) 30: [----------] 504 tests from Combinations/NbnxmKernelTest (560 ms total) 30: 30: [----------] 4 tests from WithParameters/PlainPairlistTest 30: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 30: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/0 (1 ms) 30: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 30: ./src/gromacs/nbnxm/tests/plainpairlist.cpp:235: Skipped 30: Cannot test or generate data for 4xN kernels without suitable SIMD support 30: 30: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 (0 ms) 30: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 30: ./src/gromacs/nbnxm/tests/plainpairlist.cpp:241: Skipped 30: Cannot test or generate data for 2xNN kernels without suitable SIMD support 30: 30: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 (0 ms) 30: [ RUN ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 30: [ OK ] WithParameters/PlainPairlistTest.ContainsAllPairs/3 (1 ms) 30: [----------] 4 tests from WithParameters/PlainPairlistTest (3 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 529 tests from 4 test suites ran. (564 ms total) 30: [ PASSED ] 95 tests. 30: [ SKIPPED ] 434 tests, listed below: 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_1x1_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_plain_C_4x4_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD4xM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombReactionField_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwald_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_NoEnergies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_Energies_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabYes_ThreeEnergyGroups_CoulombEwaldTwin_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombNone_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombLB 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwCutCombNone 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwForceSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwPotSwitch 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_NoEnergies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_Energies_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] Combinations/NbnxmKernelTest.WorksWith/type_SIMD2xMM_TabNo_ThreeEnergyGroups_CoulombFmm_VdwEwaldCombGeom 30: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/1 30: [ SKIPPED ] WithParameters/PlainPairlistTest.ContainsAllPairs/2 30/103 Test #30: NbnxmTests ................................ Passed 0.64 sec test 31 Start 31: NbnxmGpuTests 31: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nbnxm-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/NbnxmGpuTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests 31: Test timeout computed to be: 30 31: This test program does NOT link in any test case. Please make sure this is intended. 31: [==========] Running 0 tests from 0 test suites. 31: [==========] 0 tests from 0 test suites ran. (0 ms total) 31: [ PASSED ] 0 tests. 31/103 Test #31: NbnxmGpuTests ............................. Passed 0.04 sec test 32 Start 32: GmxlibTests 32: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/GmxlibTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests 32: Test timeout computed to be: 30 32: [==========] Running 78 tests from 2 test suites. 32: [----------] Global test environment set-up. 32: [----------] 72 tests from NBInteraction/NonbondedFepTest 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (1 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 32: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 32: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 32: [----------] 72 tests from NBInteraction/NonbondedFepTest (24 ms total) 32: 32: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 32: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 32: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 32: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (2 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 78 tests from 2 test suites ran. (26 ms total) 32: [ PASSED ] 78 tests. 32/103 Test #32: GmxlibTests ............................... Passed 0.07 sec test 33 Start 33: GmxlibGpuTests 33: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/nonbonded-fep-gpu-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/GmxlibGpuTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/nbnxm/tests 33: Test timeout computed to be: 30 33: This test program does NOT link in any test case. Please make sure this is intended. 33: [==========] Running 0 tests from 0 test suites. 33: [==========] 0 tests from 0 test suites ran. (0 ms total) 33: [ PASSED ] 0 tests. 33/103 Test #33: GmxlibGpuTests ............................ Passed 0.04 sec test 34 Start 34: CommandLineUnitTests 34: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests 34: Test timeout computed to be: 30 34: [==========] Running 60 tests from 7 test suites. 34: [----------] Global test environment set-up. 34: [----------] 3 tests from CommandLineHelpModuleTest 34: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 34: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 34: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 34: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 34: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 34: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 34: [----------] 3 tests from CommandLineHelpModuleTest (3 ms total) 34: 34: [----------] 7 tests from CommandLineHelpWriterTest 34: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 34: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 34: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 34: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 34: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 34: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 34: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 34: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 34: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 34: [----------] 7 tests from CommandLineHelpWriterTest (3 ms total) 34: 34: [----------] 6 tests from CommandLineModuleManagerTest 34: [ RUN ] CommandLineModuleManagerTest.RunsModule 34: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 34: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 34: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 34: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 34: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 34: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 34: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 34: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 34: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 34: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 34: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 34: [----------] 6 tests from CommandLineModuleManagerTest (1 ms total) 34: 34: [----------] 13 tests from CommandLineParserTest 34: [ RUN ] CommandLineParserTest.HandlesSingleValues 34: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 34: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 34: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 34: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 34: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 34: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesString 34: [ OK ] CommandLineParserTest.HandlesString (0 ms) 34: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 34: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 34: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 34: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 34: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 34: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 34: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 34: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 34: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 34: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 34: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 34: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 34: [----------] 13 tests from CommandLineParserTest (1 ms total) 34: 34: [----------] 6 tests from CommandLineProgramContextTest 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 34: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 34: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 34: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 34: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 34: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 34: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 34: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 34: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 34: 34: [----------] 3 tests from OutputNamesTest 34: [ RUN ] OutputNamesTest.CanBeSuffixed 34: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 34: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 34: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 34: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 34: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 34: [----------] 3 tests from OutputNamesTest (0 ms total) 34: 34: [----------] 22 tests from ParseCommonArgsTest 34: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 34: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 34: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 34: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 34: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 34: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 34: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 34: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 34: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 34: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 34: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 34: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 34: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 34: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 34: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 34: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 34: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 34: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 34: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 34: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 34: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 34: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 34: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 34: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 34: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 34: Value is /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 34: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 34: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 34: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 34: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 34: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (9 ms) 34: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 34: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 34: [----------] 22 tests from ParseCommonArgsTest (12 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 60 tests from 7 test suites ran. (23 ms total) 34: [ PASSED ] 60 tests. 34/103 Test #34: CommandLineUnitTests ...................... Passed 0.05 sec test 35 Start 35: DomDecTests 35: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/DomDecTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/domdec/tests 35: Test timeout computed to be: 30 35: [==========] Running 9 tests from 2 test suites. 35: [----------] Global test environment set-up. 35: [----------] 7 tests from HashedMap 35: [ RUN ] HashedMap.InsertsFinds 35: [ OK ] HashedMap.InsertsFinds (0 ms) 35: [ RUN ] HashedMap.NegativeKeysWork 35: [ OK ] HashedMap.NegativeKeysWork (0 ms) 35: [ RUN ] HashedMap.InsertsErases 35: [ OK ] HashedMap.InsertsErases (0 ms) 35: [ RUN ] HashedMap.InsertsOrAssigns 35: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 35: [ RUN ] HashedMap.Clears 35: [ OK ] HashedMap.Clears (0 ms) 35: [ RUN ] HashedMap.LinkedEntries 35: [ OK ] HashedMap.LinkedEntries (0 ms) 35: [ RUN ] HashedMap.ResizesTable 35: [ OK ] HashedMap.ResizesTable (0 ms) 35: [----------] 7 tests from HashedMap (0 ms total) 35: 35: [----------] 2 tests from LocalAtomSetManager 35: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 35: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 35: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 35: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 35: [----------] 2 tests from LocalAtomSetManager (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 9 tests from 2 test suites ran. (0 ms total) 35: [ PASSED ] 9 tests. 35/103 Test #35: DomDecTests ............................... Passed 0.02 sec test 36 Start 36: DomDecMpiTests 36: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/domdec/tests 36: Test timeout computed to be: 30 36: [==========] Running 8 tests from 1 test suite. 36: [----------] Global test environment set-up. 36: [----------] 8 tests from Works/HaloExchangeTest 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/0 36: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/0 (3 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/1 36: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/1 (0 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/2 36: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/2 (0 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnCpu/3 36: [ OK ] Works/HaloExchangeTest.WithParametersOnCpu/3 (0 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/0 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 1 pulse 36: 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 (1 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/1 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 1D halo with 2 pulses 36: 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 (0 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/2 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 1 pulse in each dimension 36: 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 (0 ms) 36: [ RUN ] Works/HaloExchangeTest.WithParametersOnGpu/3 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 36: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:653: Skipped 36: With thread-MPI, GPU halo exchange is only supported on CUDA 36: Google Test trace: 36: ./src/gromacs/domdec/tests/haloexchange_mpi.cpp:648: Testing 2D halo with 2 pulses in first dimension 36: 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 (0 ms) 36: [----------] 8 tests from Works/HaloExchangeTest (8 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 8 tests from 1 test suite ran. (8 ms total) 36: [ PASSED ] 4 tests. 36: [ SKIPPED ] 4 tests, listed below: 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/0 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/1 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/2 36: [ SKIPPED ] Works/HaloExchangeTest.WithParametersOnGpu/3 36/103 Test #36: DomDecMpiTests ............................ Passed 0.05 sec test 37 Start 37: EwaldUnitTests 37: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/ewald/tests 37: Test timeout computed to be: 30 37: [==========] Running 407 tests from 9 test suites. 37: [----------] Global test environment set-up. 37: [----------] 6 tests from SeparatePmeRanksPermittedTest 37: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 37: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 37: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 37: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 37: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 37: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 37: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 37: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 37: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 37: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 37: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 37: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 37: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 37: 37: [----------] 108 tests from Pme_SplineAndSpreadTest 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (6 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (6 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (6 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (2 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (3 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (4 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (5 ms) 37: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 37: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (5 ms) 37: [----------] 108 tests from Pme_SplineAndSpreadTest (234 ms total) 37: 37: [----------] 64 tests from Pme_SolveTest 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [----------] 64 tests from Pme_SolveTest (30 ms total) 37: 37: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (10 ms total) 37: 37: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 37: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 37: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (17 ms total) 37: 37: [----------] 64 tests from PmeDiffEps_SolveTest 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (1 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: ./src/gromacs/ewald/tests/pmesolvetest.cpp:286: Skipped 37: Test is being skipped because: 37: CPU PME solve does not implement XYZ grid ordering 37: 37: 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 37: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 37: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 37: [----------] 64 tests from PmeDiffEps_SolveTest (29 ms total) 37: 37: [----------] 72 tests from Pme_GatherTest 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 37: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 37: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 37: [----------] 72 tests from Pme_GatherTest (43 ms total) 37: 37: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 37: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 37: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 37: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 37: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 37: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 37: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 37: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 37: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (3 ms) 37: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 37: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 37: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (4 ms total) 37: 37: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (3 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (3 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (3 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (4 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (4 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (4 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (4 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (4 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (3 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (7 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (3 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (3 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (3 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (2 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (4 ms) 37: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 37: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 37: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (88 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 407 tests from 9 test suites ran. (459 ms total) 37: [ PASSED ] 311 tests. 37: [ SKIPPED ] 96 tests, listed below: 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 37: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 37/103 Test #37: EwaldUnitTests ............................ Passed 0.53 sec test 38 Start 38: FFTUnitTests 38: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fft/tests 38: Test timeout computed to be: 1920 38: [==========] Running 15 tests from 4 test suites. 38: [----------] Global test environment set-up. 38: [----------] 2 tests from ManyFFTTest 38: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 38: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (42 ms) 38: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 38: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (10 ms) 38: [----------] 2 tests from ManyFFTTest (53 ms total) 38: 38: [----------] 1 test from FFTTest 38: [ RUN ] FFTTest.Real2DLength18_15Test 38: [ OK ] FFTTest.Real2DLength18_15Test (3 ms) 38: [----------] 1 test from FFTTest (3 ms total) 38: 38: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 38: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 38: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 38: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 38: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (1 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 38: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 38: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 38: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 38: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 38: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (5 ms) 38: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 38: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (8 ms) 38: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (23 ms total) 38: 38: [----------] 2 tests from Works/ParameterizedFFTTest3D 38: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 38: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (1 ms) 38: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 38: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (1 ms) 38: [----------] 2 tests from Works/ParameterizedFFTTest3D (4 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 15 tests from 4 test suites ran. (84 ms total) 38: [ PASSED ] 15 tests. 38/103 Test #38: FFTUnitTests .............................. Passed 0.13 sec test 39 Start 39: FmmInterfaceUnitTests 39: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/fmm-interface-tests "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/FmmInterfaceUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fmm/tests 39: Test timeout computed to be: 30 39: [==========] Running 18 tests from 4 test suites. 39: [----------] Global test environment set-up. 39: [----------] 10 tests from FmmMdpOptionsTest 39: [ RUN ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive 39: [ OK ] FmmMdpOptionsTest.ThrowsOnExaFmmOptionsAccessWhenInactive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive 39: [ OK ] FmmMdpOptionsTest.ThrowsOnFMSolvrOptionsAccessWhenInactive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive 39: [ OK ] FmmMdpOptionsTest.ExaFmmOptionsMatchDefaultsWhenActive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive 39: [ OK ] FmmMdpOptionsTest.FMSolvrOptionsMatchDefaultsWhenActive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues 39: [ OK ] FmmMdpOptionsTest.DirectProviderMethodReturnsCorrectValues (0 ms) 39: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder 39: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultExaFmmOrder (0 ms) 39: [ RUN ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder 39: [ OK ] FmmMdpOptionsTest.ParsesNonDefaultFMSolvrOrder (0 ms) 39: [ RUN ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive 39: [ OK ] FmmMdpOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive 39: [ OK ] FmmMdpOptionsTest.OutputDefaultExaFmmValuesWhenActive (0 ms) 39: [ RUN ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive 39: [ OK ] FmmMdpOptionsTest.OutputDefaultFMSolvrValuesWhenActive (0 ms) 39: [----------] 10 tests from FmmMdpOptionsTest (2 ms total) 39: 39: [----------] 4 tests from FmmMdpValidatorTest 39: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings 39: 39: ERROR 1 [file unknown]: 39: ExaFMM expansion order must be greater than 0. 39: 39: 39: ERROR 1 [file unknown]: 39: ExaFMM direct range must be 2 when using GROMACS as a direct provider. 39: 39: 39: ERROR 1 [file unknown]: 39: Adaptive tree cannot be used for FMM when GROMACS is the direct provider. 39: Use a uniform tree instead. 39: 39: 39: ERROR 1 [file unknown]: 39: Maximum particles per cell for FMM must be set to a positive value when 39: using an adaptive tree. 39: 39: 39: ERROR 1 [file unknown]: 39: Tree depth for FMM is determined based on the domain decomposition grid 39: when using GROMACS as the direct provider and should not be set by the 39: user. 39: 39: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidExaFmmSettings (0 ms) 39: [ RUN ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings 39: 39: ERROR 1 [file unknown]: 39: FMSolvr tree depth must be greater than or equal to 0. 39: 39: [ OK ] FmmMdpValidatorTest.ReportsErrorsForInvalidFMSolvrSettings (0 ms) 39: [ RUN ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings 39: [ OK ] FmmMdpValidatorTest.ReportsNoErrorsOnValidMdpSettings (0 ms) 39: [ RUN ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm 39: 39: ERROR 1 [file unknown]: 39: FMM requires Coulomb interaction type to be FMM, but got PME 39: 39: [ OK ] FmmMdpValidatorTest.ReportsErrorWhenColumbTypeIsNotFmm (0 ms) 39: [----------] 4 tests from FmmMdpValidatorTest (1 ms total) 39: 39: [----------] 1 test from FmmForceProviderTest 39: [ RUN ] FmmForceProviderTest.ThrowsWhenConstructingStub 39: [ OK ] FmmForceProviderTest.ThrowsWhenConstructingStub (0 ms) 39: [----------] 1 test from FmmForceProviderTest (0 ms total) 39: 39: [----------] 3 tests from FmmForceProviderBuilderTest 39: [ RUN ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady 39: [ OK ] FmmForceProviderBuilderTest.ThrowsIfBuilderNotReady (0 ms) 39: [ RUN ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup 39: [ OK ] FmmForceProviderBuilderTest.BuildsWithMinimalSetup (0 ms) 39: [ RUN ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider 39: [ OK ] FmmForceProviderBuilderTest.ThrowIfFmmNotNotifiedOfDirectProvider (0 ms) 39: [----------] 3 tests from FmmForceProviderBuilderTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 18 tests from 4 test suites ran. (4 ms total) 39: [ PASSED ] 18 tests. 39/103 Test #39: FmmInterfaceUnitTests ..................... Passed 0.03 sec test 40 Start 40: GpuUtilsUnitTests 40: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests 40: Test timeout computed to be: 30 40: [==========] Running 67 tests from 22 test suites. 40: [----------] Global test environment set-up. 40: [----------] 2 tests from ClfftInitializer 40: [ RUN ] ClfftInitializer.SingleInitializationWorks 40: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 40: [ RUN ] ClfftInitializer.TwoInitializationsWork 40: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 40: [----------] 2 tests from ClfftInitializer (0 ms total) 40: 40: [----------] 1 test from DevicesAvailable 40: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 40: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 40: [----------] 1 test from DevicesAvailable (0 ms total) 40: 40: [----------] 1 test from DeviceStreamManagerTest 40: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 40: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 40: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 40: 40: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 40: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 40: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 40: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 40: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 40: 40: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 40: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 40: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 40: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 40: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 40: 40: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 40: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 40: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 40: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 40: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 40: 40: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 40: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 40: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 40: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 40: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 40: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 40: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 40: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 40: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 40: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 40: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 40: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 40: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 40: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 40: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 40: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 40: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 40: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 40: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 40: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 40: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 40: 40: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 40: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 40: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 40: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 40: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/0.Swap 40: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/0.Comparison 40: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 40: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 40: 40: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 40: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 40: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 40: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 40: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/1.Swap 40: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/1.Comparison 40: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 40: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 40: 40: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 40: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 40: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 40: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 40: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/2.Swap 40: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/2.Comparison 40: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 40: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 40: 40: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 40: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 40: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 40: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 40: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/3.Swap 40: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 40: [ RUN ] HostAllocatorTestNoMem/3.Comparison 40: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 40: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 40: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 40: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 40: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 40: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 40: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 40: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 40: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 40: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 40: 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 40: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 40: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 40: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 40: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator 40: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstructionOfStructHoldingAHostVectorDoesNotCopyTheAllocator (0 ms) 40: [----------] 3 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 40: 40: [----------] 1 test from HostAllocatorUntypedTest 40: [ RUN ] HostAllocatorUntypedTest.Comparison 40: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 40: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 40: 40: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 40: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 40: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 40: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 40: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/0.Move 40: [ OK ] AllocatorTest/0.Move (0 ms) 40: [----------] 4 tests from AllocatorTest/0 (0 ms total) 40: 40: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 40: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 40: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 40: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 40: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/1.Move 40: [ OK ] AllocatorTest/1.Move (0 ms) 40: [----------] 4 tests from AllocatorTest/1 (0 ms total) 40: 40: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator,gmx::HostAllocationPolicy> 40: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 40: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 40: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 40: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/2.Move 40: [ OK ] AllocatorTest/2.Move (0 ms) 40: [----------] 4 tests from AllocatorTest/2 (0 ms total) 40: 40: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 40: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 40: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 40: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 40: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 40: [ RUN ] AllocatorTest/3.Move 40: [ OK ] AllocatorTest/3.Move (0 ms) 40: [----------] 4 tests from AllocatorTest/3 (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 67 tests from 22 test suites ran. (1 ms total) 40: [ PASSED ] 67 tests. 40/103 Test #40: GpuUtilsUnitTests ......................... Passed 0.05 sec test 41 Start 41: GpuUtilsMpiTests 41: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/gpu_utils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/GpuUtilsMpiTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gpu_utils/tests 41: Test timeout computed to be: 30 41: [==========] Running 15 tests from 1 test suite. 41: [----------] Global test environment set-up. 41: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:208: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:243: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:278: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message (0 ms) 41: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/0_values_in_message 41: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/1_values_in_message 41: [ DISABLED ] WorksOnParameters/GpuAwareMpiTest.DISABLED_SendFromDeviceBufferToPinnedHostBuffer/12000_values_in_message 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:358: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message (0 ms) 41: [ RUN ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: ./src/gromacs/gpu_utils/tests/gpu_aware_mpi.cpp:389: Skipped 41: Can only test GPU-aware MPI on a build with an MPI library 41: Can only test GPU-aware MPI in a build with GPU support 41: Can only test GPU-aware MPI on ranks with available GPUs 41: GPU-aware MPI is not supported on at least one device and/or rank 41: 41: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message (0 ms) 41: [----------] 15 tests from WorksOnParameters/GpuAwareMpiTest (6 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 15 tests from 1 test suite ran. (6 ms total) 41: [ PASSED ] 0 tests. 41: [ SKIPPED ] 15 tests, listed below: 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/0_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/1_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromUnpinnedHostBufferToDeviceBuffer/12000_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/0_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/1_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromPinnedHostBufferToDeviceBuffer/12000_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/0_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/1_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToUnpinnedHostBuffer/12000_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/0_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/1_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.SendFromDeviceBufferToDeviceBuffer/12000_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/0_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/1_values_in_message 41: [ SKIPPED ] WorksOnParameters/GpuAwareMpiTest.IrecvSendPair/12000_values_in_message 41: 41: YOU HAVE 3 DISABLED TESTS 41: 41/103 Test #41: GpuUtilsMpiTests .......................... Passed 0.05 sec test 42 Start 42: HardwareUnitTests 42: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/hardware/tests 42: Test timeout computed to be: 30 42: [==========] Running 22 tests from 10 test suites. 42: [----------] Global test environment set-up. 42: [----------] 1 test from CpuInfoTest 42: [ RUN ] CpuInfoTest.SupportLevel 42: [ OK ] CpuInfoTest.SupportLevel (0 ms) 42: [----------] 1 test from CpuInfoTest (0 ms total) 42: 42: [----------] 4 tests from HardwareTopologyTest 42: [ RUN ] HardwareTopologyTest.Execute 42: [ OK ] HardwareTopologyTest.Execute (15 ms) 42: [ RUN ] HardwareTopologyTest.HwlocExecute 42: [ OK ] HardwareTopologyTest.HwlocExecute (14 ms) 42: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 42: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (14 ms) 42: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 42: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (14 ms) 42: [----------] 4 tests from HardwareTopologyTest (58 ms total) 42: 42: [----------] 1 test from DevicesManagerTest 42: [ RUN ] DevicesManagerTest.Serialization 42: [ OK ] DevicesManagerTest.Serialization (0 ms) 42: [ DISABLED ] DevicesManagerTest.DISABLED_DetectsUuid 42: [----------] 1 test from DevicesManagerTest (0 ms total) 42: 42: [----------] 1 test from UuidStringTest 42: [ RUN ] UuidStringTest.Works 42: [ OK ] UuidStringTest.Works (0 ms) 42: [----------] 1 test from UuidStringTest (0 ms total) 42: 42: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 42: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 42: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (2 ms) 42: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 42: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 42: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 42: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (1 ms) 42: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 42: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (1 ms) 42: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 42: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (1 ms) 42: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (8 ms total) 42: 42: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 42: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 42: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (2 ms) 42: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 42: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (40 ms) 42: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 42: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (1 ms) 42: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 42: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (1 ms) 42: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 42: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (1 ms) 42: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (47 ms total) 42: 42: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 42: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 42: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 42: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 42: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 42: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (3 ms total) 42: 42: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 42: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 42: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (2 ms) 42: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (2 ms total) 42: 42: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 42: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 42: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (4 ms) 42: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (4 ms total) 42: 42: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 42: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 42: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (20 ms) 42: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (21 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 22 tests from 10 test suites ran. (146 ms total) 42: [ PASSED ] 22 tests. 42: 42: YOU HAVE 1 DISABLED TEST 42: 42/103 Test #42: HardwareUnitTests ......................... Passed 0.18 sec test 43 Start 43: MathUnitTests 43: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/math/tests 43: Test timeout computed to be: 30 43: [==========] Running 293 tests from 40 test suites. 43: [----------] Global test environment set-up. 43: [----------] 1 test from EmptyArrayRefWithPaddingTest 43: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 43: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 43: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 43: 43: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 43: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 43: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 43: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 43: 43: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 43: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 43: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 43: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 43: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 43: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 43: 43: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 43: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 43: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 43: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 43: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 43: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 43: 43: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 43: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 43: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 43: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 43: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 43: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 43: 43: [----------] 2 tests from InvertBoxMatrixTest 43: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 43: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 43: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 43: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 43: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 43: 43: [----------] 8 tests from ComplexNumberTest 43: [ RUN ] ComplexNumberTest.RealComplexMultiply 43: [ OK ] ComplexNumberTest.RealComplexMultiply (0 ms) 43: [ RUN ] ComplexNumberTest.RealComplexExp 43: [ OK ] ComplexNumberTest.RealComplexExp (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexAdd 43: [ OK ] ComplexNumberTest.ComplexAdd (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexSubtract 43: [ OK ] ComplexNumberTest.ComplexSubtract (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexMultiply 43: [ OK ] ComplexNumberTest.ComplexMultiply (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexDivision 43: [ OK ] ComplexNumberTest.ComplexDivision (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexConjugate 43: [ OK ] ComplexNumberTest.ComplexConjugate (0 ms) 43: [ RUN ] ComplexNumberTest.ComplexAbs2 43: [ OK ] ComplexNumberTest.ComplexAbs2 (0 ms) 43: [----------] 8 tests from ComplexNumberTest (2 ms total) 43: 43: [----------] 11 tests from TranslateAndScaleTest 43: [ RUN ] TranslateAndScaleTest.identityTransformation 43: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 43: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 43: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 43: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 43: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 43: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 43: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 43: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingIdentity 43: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 43: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 43: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 43: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 43: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 43: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 43: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 43: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 43: 43: [----------] 3 tests from AffineTransformationTest 43: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 43: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 43: [ RUN ] AffineTransformationTest.applyTransformationToVectors 43: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 43: [ RUN ] AffineTransformationTest.retrieveGradient 43: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 43: [----------] 3 tests from AffineTransformationTest (0 ms total) 43: 43: [----------] 14 tests from DensitySimilarityTest 43: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 43: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 43: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 43: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 43: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 43: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 43: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 43: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 43: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 43: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 43: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 43: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 43: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (104 ms) 43: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 43: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (103 ms) 43: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 43: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (4 ms) 43: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 43: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (36 ms) 43: [ RUN ] DensitySimilarityTest.NormalizationCorrect 43: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 43: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 43: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 43: [----------] 14 tests from DensitySimilarityTest (251 ms total) 43: 43: [----------] 6 tests from StructureSimilarityTest 43: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 43: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 43: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 43: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 43: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 43: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 43: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 43: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 43: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 43: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 43: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 43: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 43: [----------] 6 tests from StructureSimilarityTest (0 ms total) 43: 43: [----------] 8 tests from ExponentialMovingAverage 43: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 43: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 43: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 43: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 43: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 43: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 43: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 43: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 43: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 43: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 43: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 43: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 43: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 43: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 43: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 43: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 43: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 43: 43: [----------] 21 tests from FunctionTest 43: [ RUN ] FunctionTest.StaticLog2 43: [ OK ] FunctionTest.StaticLog2 (0 ms) 43: [ RUN ] FunctionTest.Log2I32Bit 43: [ OK ] FunctionTest.Log2I32Bit (1 ms) 43: [ RUN ] FunctionTest.Log2I64Bit 43: [ OK ] FunctionTest.Log2I64Bit (0 ms) 43: [ RUN ] FunctionTest.GreatestCommonDivisor 43: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 43: [ RUN ] FunctionTest.InvsqrtFloat 43: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 43: [ RUN ] FunctionTest.InvsqrtDouble 43: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 43: [ RUN ] FunctionTest.InvsqrtInteger 43: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 43: [ RUN ] FunctionTest.InvcbrtFloat 43: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 43: [ RUN ] FunctionTest.InvcbrtDouble 43: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 43: [ RUN ] FunctionTest.InvcbrtInteger 43: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 43: [ RUN ] FunctionTest.SixthrootFloat 43: [ OK ] FunctionTest.SixthrootFloat (0 ms) 43: [ RUN ] FunctionTest.SixthrootDouble 43: [ OK ] FunctionTest.SixthrootDouble (0 ms) 43: [ RUN ] FunctionTest.SixthrootInteger 43: [ OK ] FunctionTest.SixthrootInteger (0 ms) 43: [ RUN ] FunctionTest.InvsixthrootFloat 43: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 43: [ RUN ] FunctionTest.InvsixthrootDouble 43: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 43: [ RUN ] FunctionTest.InvsixthrootInteger 43: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 43: [ RUN ] FunctionTest.Powers 43: [ OK ] FunctionTest.Powers (0 ms) 43: [ RUN ] FunctionTest.ErfInvFloat 43: [ OK ] FunctionTest.ErfInvFloat (0 ms) 43: [ RUN ] FunctionTest.ErfInvDouble 43: [ OK ] FunctionTest.ErfInvDouble (0 ms) 43: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 43: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 43: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 43: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 43: [----------] 21 tests from FunctionTest (6 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/0, where TypeParam = signed char 43: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/0.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/0.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/0 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 43: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/1.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/1.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/1 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/2, where TypeParam = short 43: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/2.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/2.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/2 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/3, where TypeParam = unsigned short 43: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/3.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/3.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/3 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/4, where TypeParam = int 43: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/4.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/4.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/4 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/5, where TypeParam = unsigned int 43: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/5.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/5.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/5 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/6, where TypeParam = long 43: [ RUN ] FunctionTestIntegerTypes/6.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/6.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/6.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/6.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/6 (0 ms total) 43: 43: [----------] 2 tests from FunctionTestIntegerTypes/7, where TypeParam = unsigned long 43: [ RUN ] FunctionTestIntegerTypes/7.IsPowerOfTwo 43: [ OK ] FunctionTestIntegerTypes/7.IsPowerOfTwo (0 ms) 43: [ RUN ] FunctionTestIntegerTypes/7.DivideRoundUp 43: [ OK ] FunctionTestIntegerTypes/7.DivideRoundUp (0 ms) 43: [----------] 2 tests from FunctionTestIntegerTypes/7 (0 ms total) 43: 43: [----------] 4 tests from GaussianOn1DLattice 43: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 43: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 43: [ RUN ] GaussianOn1DLattice.isCorrect 43: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 43: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 43: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 43: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 43: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 43: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 43: 43: [----------] 9 tests from GaussTransformTest 43: [ RUN ] GaussTransformTest.isZeroUponConstruction 43: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 43: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 43: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 43: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 43: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 43: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 43: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 43: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 43: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 43: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 43: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 43: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 43: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 43: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 43: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 43: [ RUN ] GaussTransformTest.view 43: [ OK ] GaussTransformTest.view (0 ms) 43: [----------] 9 tests from GaussTransformTest (0 ms total) 43: 43: [----------] 3 tests from DensityFittingForce 43: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 43: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 43: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 43: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 43: [ RUN ] DensityFittingForce.pullsTowardsDerivative 43: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 43: [----------] 3 tests from DensityFittingForce (0 ms total) 43: 43: [----------] 2 tests from InvertMatrixTest 43: [ RUN ] InvertMatrixTest.IdentityIsImpotent 43: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 43: [ RUN ] InvertMatrixTest.ComputesInverse 43: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 43: [----------] 2 tests from InvertMatrixTest (0 ms total) 43: 43: [----------] 28 tests from MatrixTest 43: [ RUN ] MatrixTest.canSetFromArray 43: [ OK ] MatrixTest.canSetFromArray (0 ms) 43: [ RUN ] MatrixTest.canSetStaticallyFromList 43: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 43: [ RUN ] MatrixTest.canSetStaticallySingleValue 43: [ OK ] MatrixTest.canSetStaticallySingleValue (0 ms) 43: [ RUN ] MatrixTest.canConstructAndFill 43: [ OK ] MatrixTest.canConstructAndFill (0 ms) 43: [ RUN ] MatrixTest.canSetValues 43: [ OK ] MatrixTest.canSetValues (0 ms) 43: [ RUN ] MatrixTest.canCopyAssign 43: [ OK ] MatrixTest.canCopyAssign (0 ms) 43: [ RUN ] MatrixTest.canSwap 43: [ OK ] MatrixTest.canSwap (0 ms) 43: [ RUN ] MatrixTest.staticMultiDimArrayExtent 43: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 43: [ RUN ] MatrixTest.canAddMatrix 43: [ OK ] MatrixTest.canAddMatrix (0 ms) 43: [ RUN ] MatrixTest.canAddAssignMatrix 43: [ OK ] MatrixTest.canAddAssignMatrix (0 ms) 43: [ RUN ] MatrixTest.canSubtractMatrix 43: [ OK ] MatrixTest.canSubtractMatrix (0 ms) 43: [ RUN ] MatrixTest.canSubtractAssignMatrix 43: [ OK ] MatrixTest.canSubtractAssignMatrix (0 ms) 43: [ RUN ] MatrixTest.canNegateMatrix 43: [ OK ] MatrixTest.canNegateMatrix (0 ms) 43: [ RUN ] MatrixTest.MatrixScalarMultiplication 43: [ OK ] MatrixTest.MatrixScalarMultiplication (0 ms) 43: [ RUN ] MatrixTest.MatrixScalarDivision 43: [ OK ] MatrixTest.MatrixScalarDivision (0 ms) 43: [ RUN ] MatrixTest.MatrixVectorMultiplicationOperator 43: [ OK ] MatrixTest.MatrixVectorMultiplicationOperator (0 ms) 43: [ RUN ] MatrixTest.MatrixMatrixInnerProduct 43: [ OK ] MatrixTest.MatrixMatrixInnerProduct (0 ms) 43: [ RUN ] MatrixTest.MatrixMatrixMultiplication 43: [ OK ] MatrixTest.MatrixMatrixMultiplication (0 ms) 43: [ RUN ] MatrixTest.determinantWorks 43: [ OK ] MatrixTest.determinantWorks (0 ms) 43: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 43: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 43: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 43: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 43: [ RUN ] MatrixTest.traceWorks 43: [ OK ] MatrixTest.traceWorks (0 ms) 43: [ RUN ] MatrixTest.transposeWorks 43: [ OK ] MatrixTest.transposeWorks (0 ms) 43: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 43: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 43: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 43: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 43: [ RUN ] MatrixTest.canFillLegacyMatrix 43: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 43: [ RUN ] MatrixTest.IdentityMatrix 43: [ OK ] MatrixTest.IdentityMatrix (0 ms) 43: [ RUN ] MatrixTest.DiagonalMatrix 43: [ OK ] MatrixTest.DiagonalMatrix (0 ms) 43: [----------] 28 tests from MatrixTest (0 ms total) 43: 43: [----------] 25 tests from MultiDimArrayTest 43: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 43: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 43: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 43: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 43: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 43: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 43: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 43: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 43: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 43: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 43: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 43: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 43: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.canSwapStatic 43: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 43: [ RUN ] MultiDimArrayTest.canSwapDynamic 43: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 43: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 43: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 43: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 43: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 43: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 43: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 43: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 43: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 43: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 43: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 43: [ RUN ] MultiDimArrayTest.conversionToView 43: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 43: [ RUN ] MultiDimArrayTest.conversionToConstView 43: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 43: [ RUN ] MultiDimArrayTest.viewBegin 43: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 43: [ RUN ] MultiDimArrayTest.viewEnd 43: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 43: [ RUN ] MultiDimArrayTest.constViewConstBegin 43: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 43: [ RUN ] MultiDimArrayTest.constViewConstEnd 43: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 43: [----------] 25 tests from MultiDimArrayTest (0 ms total) 43: 43: [----------] 4 tests from MultiDimArrayToMdSpanTest 43: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 43: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 43: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 43: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 43: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 43: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 43: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 43: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 43: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 43: 43: [----------] 9 tests from NelderMeadSimplexTest 43: [ RUN ] NelderMeadSimplexTest.BestVertex 43: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 43: [ RUN ] NelderMeadSimplexTest.WorstVertex 43: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 43: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 43: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 43: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 43: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 43: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 43: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 43: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 43: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 43: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 43: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 43: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 43: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 43: [ RUN ] NelderMeadSimplexTest.OrientedLength 43: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 43: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 43: 43: [----------] 2 tests from NelderMead 43: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 43: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 43: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 43: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 43: [----------] 2 tests from NelderMead (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 43: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.ResizeWorks 43: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.ReserveWorks 43: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/0.CanCopyAssign 43: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/0.CanMoveAssign 43: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/0.CanSwap 43: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 43: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.ResizeWorks 43: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.ReserveWorks 43: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/1.CanCopyAssign 43: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/1.CanMoveAssign 43: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/1.CanSwap 43: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 43: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.ResizeWorks 43: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.ReserveWorks 43: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/2.CanCopyAssign 43: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/2.CanMoveAssign 43: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/2.CanSwap 43: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 43: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.ResizeWorks 43: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.ReserveWorks 43: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/3.CanCopyAssign 43: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/3.CanMoveAssign 43: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/3.CanSwap 43: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 43: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.ResizeWorks 43: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.ReserveWorks 43: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/4.CanCopyAssign 43: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/4.CanMoveAssign 43: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/4.CanSwap 43: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 43: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.ResizeWorks 43: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.ReserveWorks 43: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/5.CanCopyAssign 43: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/5.CanMoveAssign 43: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/5.CanSwap 43: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 43: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.ResizeWorks 43: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.ReserveWorks 43: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/6.CanCopyAssign 43: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/6.CanMoveAssign 43: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/6.CanSwap 43: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 43: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.ResizeWorks 43: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.ReserveWorks 43: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/7.CanCopyAssign 43: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/7.CanMoveAssign 43: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/7.CanSwap 43: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 43: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.ResizeWorks 43: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.ReserveWorks 43: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/8.CanCopyAssign 43: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/8.CanMoveAssign 43: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/8.CanSwap 43: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 43: 43: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator,gmx::AlignedAllocationPolicy> 43: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 43: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.ResizeWorks 43: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.ReserveWorks 43: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 43: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 43: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 43: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 43: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 43: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 43: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 43: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 43: [ RUN ] PaddedVectorTest/9.CanCopyAssign 43: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 43: [ RUN ] PaddedVectorTest/9.CanMoveAssign 43: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 43: [ RUN ] PaddedVectorTest/9.CanSwap 43: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 43: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 293 tests from 40 test suites ran. (266 ms total) 43: [ PASSED ] 293 tests. 43/103 Test #43: MathUnitTests ............................. Passed 0.31 sec test 44 Start 44: MdrunUtilityUnitTests 44: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests 44: Test timeout computed to be: 30 44: [==========] Running 33 tests from 3 test suites. 44: [----------] Global test environment set-up. 44: [----------] 4 tests from MDModulesNotifierTest 44: [ RUN ] MDModulesNotifierTest.AddConsumer 44: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 44: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 44: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 44: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 44: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 44: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 44: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 44: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 44: 44: [----------] 1 test from PlainPairlistRanges 44: [ RUN ] PlainPairlistRanges.RmsdDistance 44: [ OK ] PlainPairlistRanges.RmsdDistance (0 ms) 44: [----------] 1 test from PlainPairlistRanges (0 ms total) 44: 44: [----------] 28 tests from ThreadAffinityTest 44: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 44: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 44: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 44: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 44: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 44: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 44: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 44: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 44: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 44: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 44: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 44: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 44: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 44: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 44: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 44: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask 44: [ OK ] ThreadAffinityTest.PinsWithAffinityAndShiftedMask (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 44: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 44: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 44: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 44: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 44: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndFullMask 44: [ OK ] ThreadAffinityTest.PinsWithAffinityAndFullMask (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask 44: [ OK ] ThreadAffinityTest.PinsWithAffinityAndHoleyMask (0 ms) 44: [ RUN ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall 44: [ OK ] ThreadAffinityTest.RefusesWhenAffinityMaskTooSmall (0 ms) 44: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithSmt 44: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithSmt (2 ms) 44: [ RUN ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt 44: [ OK ] ThreadAffinityTest.PinsToHalfSocketWithNoSmt (1 ms) 44: [ RUN ] ThreadAffinityTest.PinsToPCoresInHybridSystem 44: [ OK ] ThreadAffinityTest.PinsToPCoresInHybridSystem (1 ms) 44: [ RUN ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem 44: [ OK ] ThreadAffinityTest.PinsToSecondHwThreadsOnPCoresInHybridSystem (1 ms) 44: [ RUN ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem 44: [ OK ] ThreadAffinityTest.PinsToSinglePCoreInHybridSystem (1 ms) 44: [ RUN ] ThreadAffinityTest.PinsToECoresInHybridSystem 44: [ OK ] ThreadAffinityTest.PinsToECoresInHybridSystem (1 ms) 44: [ RUN ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem 44: [ OK ] ThreadAffinityTest.PinsToMixOfPAndECoresInHybridSystem (1 ms) 44: [----------] 28 tests from ThreadAffinityTest (14 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 33 tests from 3 test suites ran. (15 ms total) 44: [ PASSED ] 33 tests. 44/103 Test #44: MdrunUtilityUnitTests ..................... Passed 0.04 sec test 45 Start 45: MdrunUtilityMpiUnitTests 45: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdrunutility/tests 45: Test timeout computed to be: 30 45: [==========] Running 17 tests from 2 test suites. 45: [----------] Global test environment set-up. 45: [----------] 10 tests from ThreadAffinityMultiRankTest 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 45: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (9 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 45: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (12 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 45: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (3 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 45: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 45: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (7 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 45: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent 45: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityDifferent (3 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame 45: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySame (7 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp 45: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinitySameOpenmp (33 ms) 45: [ RUN ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken 45: [ OK ] ThreadAffinityMultiRankTest.PinsWithExternalAffinityBroken (26 ms) 45: [----------] 10 tests from ThreadAffinityMultiRankTest (109 ms total) 45: 45: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (11 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (0 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (1 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (18 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (12 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (1 ms) 45: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 45: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (1 ms) 45: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (46 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 17 tests from 2 test suites ran. (155 ms total) 45: [ PASSED ] 17 tests. 45/103 Test #45: MdrunUtilityMpiUnitTests .................. Passed 0.18 sec test 46 Start 46: MDSpanTests 46: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdspan/tests 46: Test timeout computed to be: 30 46: [==========] Running 32 tests from 7 test suites. 46: [----------] Global test environment set-up. 46: [----------] 4 tests from BasicAccessorPolicy 46: [ RUN ] BasicAccessorPolicy.Decay 46: [ OK ] BasicAccessorPolicy.Decay (0 ms) 46: [ RUN ] BasicAccessorPolicy.Access 46: [ OK ] BasicAccessorPolicy.Access (0 ms) 46: [ RUN ] BasicAccessorPolicy.Offset 46: [ OK ] BasicAccessorPolicy.Offset (0 ms) 46: [ RUN ] BasicAccessorPolicy.CopyAccessor 46: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 46: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 46: 46: [----------] 4 tests from ExtentsTest 46: [ RUN ] ExtentsTest.Construction 46: [ OK ] ExtentsTest.Construction (0 ms) 46: [ RUN ] ExtentsTest.PurelyStatic 46: [ OK ] ExtentsTest.PurelyStatic (0 ms) 46: [ RUN ] ExtentsTest.RankNought 46: [ OK ] ExtentsTest.RankNought (0 ms) 46: [ RUN ] ExtentsTest.Assignment 46: [ OK ] ExtentsTest.Assignment (0 ms) 46: [----------] 4 tests from ExtentsTest (0 ms total) 46: 46: [----------] 8 tests from MdSpanExtension 46: [ RUN ] MdSpanExtension.SlicingAllStatic 46: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 46: [ RUN ] MdSpanExtension.SlicingDynamic 46: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 46: [ RUN ] MdSpanExtension.SlicingAllStatic3D 46: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 46: [ RUN ] MdSpanExtension.SlicingEqualsView3D 46: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 46: [ RUN ] MdSpanExtension.additionWorks 46: [ OK ] MdSpanExtension.additionWorks (0 ms) 46: [ RUN ] MdSpanExtension.subtractionWorks 46: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 46: [ RUN ] MdSpanExtension.multiplicationWorks 46: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 46: [ RUN ] MdSpanExtension.divisionWorks 46: [ OK ] MdSpanExtension.divisionWorks (0 ms) 46: [----------] 8 tests from MdSpanExtension (0 ms total) 46: 46: [----------] 3 tests from LayoutTests 46: [ RUN ] LayoutTests.LayoutRightConstruction 46: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 46: [ RUN ] LayoutTests.LayoutRightProperties 46: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 46: [ RUN ] LayoutTests.LayoutRightOperator 46: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 46: [----------] 3 tests from LayoutTests (0 ms total) 46: 46: [----------] 1 test from MdSpanTest 46: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 46: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 46: [----------] 1 test from MdSpanTest (0 ms total) 46: 46: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 46: [ RUN ] MdSpanTest/0.Rank 46: [ OK ] MdSpanTest/0.Rank (0 ms) 46: [ RUN ] MdSpanTest/0.DynamicRank 46: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 46: [ RUN ] MdSpanTest/0.Extents 46: [ OK ] MdSpanTest/0.Extents (0 ms) 46: [ RUN ] MdSpanTest/0.Strides 46: [ OK ] MdSpanTest/0.Strides (0 ms) 46: [ RUN ] MdSpanTest/0.Properties 46: [ OK ] MdSpanTest/0.Properties (0 ms) 46: [ RUN ] MdSpanTest/0.Operator 46: [ OK ] MdSpanTest/0.Operator (0 ms) 46: [----------] 6 tests from MdSpanTest/0 (0 ms total) 46: 46: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan,gmx::layout_right,gmx::accessor_basic > 46: [ RUN ] MdSpanTest/1.Rank 46: [ OK ] MdSpanTest/1.Rank (0 ms) 46: [ RUN ] MdSpanTest/1.DynamicRank 46: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 46: [ RUN ] MdSpanTest/1.Extents 46: [ OK ] MdSpanTest/1.Extents (0 ms) 46: [ RUN ] MdSpanTest/1.Strides 46: [ OK ] MdSpanTest/1.Strides (0 ms) 46: [ RUN ] MdSpanTest/1.Properties 46: [ OK ] MdSpanTest/1.Properties (0 ms) 46: [ RUN ] MdSpanTest/1.Operator 46: [ OK ] MdSpanTest/1.Operator (0 ms) 46: [----------] 6 tests from MdSpanTest/1 (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 32 tests from 7 test suites ran. (0 ms total) 46: [ PASSED ] 32 tests. 46/103 Test #46: MDSpanTests ............................... Passed 0.03 sec test 47 Start 47: MdtypesUnitTest 47: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" 47: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/mdtypes/tests 47: Test timeout computed to be: 30 47: [==========] Running 98 tests from 7 test suites. 47: [----------] Global test environment set-up. 47: [----------] 4 tests from ForeingLambdaTermsDhdl 47: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 47: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 47: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 47: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 47: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 47: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 47: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 47: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 47: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 47: 47: [----------] 4 tests from ObservablesReducerTest 47: [ RUN ] ObservablesReducerTest.CanMoveAssign 47: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 47: [ RUN ] ObservablesReducerTest.CanMoveConstruct 47: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 47: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 47: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 47: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 47: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 47: [----------] 4 tests from ObservablesReducerTest (0 ms total) 47: 47: [----------] 3 tests from CheckpointDataTest 47: [ RUN ] CheckpointDataTest.SingleDataTest 47: [ OK ] CheckpointDataTest.SingleDataTest (38 ms) 47: [ RUN ] CheckpointDataTest.MultiDataTest 47: [ OK ] CheckpointDataTest.MultiDataTest (33 ms) 47: [ RUN ] CheckpointDataTest.EmptyVectorTest 47: [ OK ] CheckpointDataTest.EmptyVectorTest (0 ms) 47: [----------] 3 tests from CheckpointDataTest (72 ms total) 47: 47: [----------] 7 tests from ForceBuffers 47: [ RUN ] ForceBuffers.ConstructsUnpinned 47: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 47: [ RUN ] ForceBuffers.ConstructsPinned 47: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 47: [ RUN ] ForceBuffers.ConstructsEmpty 47: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 47: [ RUN ] ForceBuffers.ResizeWorks 47: [ OK ] ForceBuffers.ResizeWorks (0 ms) 47: [ RUN ] ForceBuffers.PaddingWorks 47: [ OK ] ForceBuffers.PaddingWorks (0 ms) 47: [ RUN ] ForceBuffers.CopyWorks 47: [ OK ] ForceBuffers.CopyWorks (0 ms) 47: [ RUN ] ForceBuffers.CopyDoesNotPin 47: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 47: [----------] 7 tests from ForceBuffers (0 ms total) 47: 47: [----------] 5 tests from MultipleTimeStepping 47: [ RUN ] MultipleTimeStepping.ChecksNumLevels 47: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 47: [ RUN ] MultipleTimeStepping.SelectsForceGroups 47: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 47: [ RUN ] MultipleTimeStepping.ChecksStepFactor 47: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 47: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 47: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 47: [ RUN ] MultipleTimeStepping.ChecksIntegrator 47: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 47: [----------] 5 tests from MultipleTimeStepping (0 ms total) 47: 47: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 47: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 47: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 47: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (2 ms total) 47: 47: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 47: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 47: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 47: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 98 tests from 7 test suites ran. (76 ms total) 47: [ PASSED ] 98 tests. 47/103 Test #47: MdtypesUnitTest ........................... Passed 0.11 sec test 48 Start 48: OnlineHelpUnitTests 48: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 48: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/onlinehelp/tests 48: Test timeout computed to be: 30 48: [==========] Running 22 tests from 4 test suites. 48: [----------] Global test environment set-up. 48: [----------] 6 tests from TextTableFormatterTest 48: [ RUN ] TextTableFormatterTest.HandlesBasicCase 48: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 48: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 48: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 48: [ RUN ] TextTableFormatterTest.HandlesIndentation 48: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 48: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 48: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 48: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 48: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 48: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 48: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 48: [----------] 6 tests from TextTableFormatterTest (2 ms total) 48: 48: [----------] 3 tests from HelpManagerTest 48: [ RUN ] HelpManagerTest.HandlesRootTopic 48: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 48: [ RUN ] HelpManagerTest.HandlesSubTopics 48: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 48: [ RUN ] HelpManagerTest.HandlesInvalidTopics 48: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 48: [----------] 3 tests from HelpManagerTest (0 ms total) 48: 48: [----------] 2 tests from HelpTopicFormattingTest 48: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 48: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 48: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 48: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 48: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 48: 48: [----------] 11 tests from HelpWriterContextTest 48: [ RUN ] HelpWriterContextTest.FormatsParagraphs 48: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 48: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 48: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 48: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsLiteralText 48: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 48: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 48: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsBulletList 48: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 48: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 48: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsGridTable 48: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 48: [ RUN ] HelpWriterContextTest.FormatsTitles 48: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 48: [----------] 11 tests from HelpWriterContextTest (3 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 22 tests from 4 test suites ran. (8 ms total) 48: [ PASSED ] 22 tests. 48/103 Test #48: OnlineHelpUnitTests ....................... Passed 0.03 sec test 49 Start 49: OptionsUnitTests 49: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/options/tests 49: Test timeout computed to be: 30 49: [==========] Running 151 tests from 21 test suites. 49: [----------] Global test environment set-up. 49: [----------] 5 tests from AbstractOptionStorageTest 49: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 49: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 49: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 49: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 49: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 49: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 49: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 49: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 49: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 49: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 49: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 49: 49: [----------] 10 tests from FileNameOptionTest 49: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 49: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 49: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 49: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 49: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 49: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 49: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 49: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 49: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 49: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 49: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 49: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 49: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 49: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 49: [----------] 10 tests from FileNameOptionTest (0 ms total) 49: 49: [----------] 16 tests from FileNameOptionManagerTest 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 49: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 49: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 49: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 49: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 49: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 49: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 49: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 49: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 49: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 49: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 49: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 49: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 49: [ RUN ] FileNameOptionManagerTest.AcceptsCompressedInputFile 49: [ OK ] FileNameOptionManagerTest.AcceptsCompressedInputFile (0 ms) 49: [----------] 16 tests from FileNameOptionManagerTest (0 ms total) 49: 49: [----------] 1 test from OptionsTest 49: [ RUN ] OptionsTest.FailsOnNonsafeStorage 49: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 49: [----------] 1 test from OptionsTest (0 ms total) 49: 49: [----------] 9 tests from OptionsAssignerTest 49: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 49: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 49: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 49: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 49: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesMissingValue 49: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesExtraValue 49: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesGroups 49: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesSections 49: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 49: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 49: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 49: [----------] 9 tests from OptionsAssignerTest (0 ms total) 49: 49: [----------] 4 tests from OptionsAssignerBooleanTest 49: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 49: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 49: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 49: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 49: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 49: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 49: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 49: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 49: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 49: 49: [----------] 13 tests from OptionsAssignerIntegerTest 49: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 49: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 49: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 49: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 49: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 49: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 49: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 49: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 49: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 49: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 49: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 49: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 49: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 49: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 49: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 49: 49: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesEmptyValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesInvalidValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesOverflow (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet 49: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresDefaultValueIfSet (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesBothDefaultValues (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.StoresToVector 49: [ OK ] OptionsAssignerUnsignedIntegerTest.StoresToVector (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectors 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectors (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorFromSingleValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 49: [ OK ] OptionsAssignerUnsignedIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 49: [----------] 13 tests from OptionsAssignerUnsignedIntegerTest (0 ms total) 49: 49: [----------] 13 tests from OptionsAssignerInt64Test 49: [ RUN ] OptionsAssignerInt64Test.StoresSingleValue 49: [ OK ] OptionsAssignerInt64Test.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesEmptyValue 49: [ OK ] OptionsAssignerInt64Test.HandlesEmptyValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesInvalidValue 49: [ OK ] OptionsAssignerInt64Test.HandlesInvalidValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesOverflow 49: [ OK ] OptionsAssignerInt64Test.HandlesOverflow (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValue 49: [ OK ] OptionsAssignerInt64Test.StoresDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.StoresDefaultValueIfSet 49: [ OK ] OptionsAssignerInt64Test.StoresDefaultValueIfSet (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet 49: [ OK ] OptionsAssignerInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesBothDefaultValues 49: [ OK ] OptionsAssignerInt64Test.HandlesBothDefaultValues (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.StoresToVector 49: [ OK ] OptionsAssignerInt64Test.StoresToVector (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesVectors 49: [ OK ] OptionsAssignerInt64Test.HandlesVectors (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue 49: [ OK ] OptionsAssignerInt64Test.HandlesVectorFromSingleValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue 49: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 49: [ OK ] OptionsAssignerInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 49: [----------] 13 tests from OptionsAssignerInt64Test (0 ms total) 49: 49: [----------] 13 tests from OptionsAssignerUnsignedInt64Test 49: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresSingleValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesEmptyValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesInvalidValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesOverflow 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesOverflow (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet 49: [ OK ] OptionsAssignerUnsignedInt64Test.StoresDefaultValueIfSet (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesDefaultValueIfSetWhenNotSet (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesBothDefaultValues (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.StoresToVector 49: [ OK ] OptionsAssignerUnsignedInt64Test.StoresToVector (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectors 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectors (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorFromSingleValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment 49: [ OK ] OptionsAssignerUnsignedInt64Test.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 49: [----------] 13 tests from OptionsAssignerUnsignedInt64Test (0 ms total) 49: 49: [----------] 5 tests from OptionsAssignerDoubleTest 49: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 49: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 49: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 49: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 49: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 49: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 49: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 49: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 49: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 49: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 49: 49: [----------] 9 tests from OptionsAssignerStringTest 49: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 49: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 49: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 49: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 49: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 49: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 49: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 49: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 49: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 49: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 49: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 49: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 49: 49: [----------] 6 tests from OptionsAssignerEnumTest 49: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 49: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 49: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 49: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 49: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 49: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 49: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 49: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 49: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 49: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 49: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 49: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 49: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 49: 49: [----------] 8 tests from RepeatingOptionSectionTest 49: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 49: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 49: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 49: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 49: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 49: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 49: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 49: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 49: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 49: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 49: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 49: 49: [----------] 1 test from TimeUnitManagerTest 49: [ RUN ] TimeUnitManagerTest.BasicOperations 49: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 49: [----------] 1 test from TimeUnitManagerTest (0 ms total) 49: 49: [----------] 4 tests from TimeUnitBehaviorTest 49: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 49: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 49: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 49: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 49: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 49: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 49: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 49: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 49: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 49: 49: [----------] 2 tests from TreeValueSupportAssignTest 49: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 49: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 49: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 49: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 49: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 49: 49: [----------] 1 test from TreeValueSupportAssignErrorTest 49: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 49: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 49: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 49: 49: [----------] 5 tests from TreeValueSupportCheckTest 49: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 49: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 49: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 49: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 49: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 49: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 49: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 49: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 49: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 49: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 49: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 49: 49: [----------] 6 tests from TreeValueSupportAdjustTest 49: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 49: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 49: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 49: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms) 49: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 49: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 49: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 49: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 49: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 49: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 49: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 49: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 49: [----------] 6 tests from TreeValueSupportAdjustTest (3 ms total) 49: 49: [----------] 7 tests from TreeValueSupportTest 49: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 49: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 49: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 49: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 49: [ RUN ] TreeValueSupportTest.SupportsInt64Option 49: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 49: [ RUN ] TreeValueSupportTest.SupportsStringOption 49: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 49: [ RUN ] TreeValueSupportTest.SupportsFloatOption 49: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 49: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 49: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 49: [ RUN ] TreeValueSupportTest.SupportsEnumOption 49: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 49: [----------] 7 tests from TreeValueSupportTest (2 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 151 tests from 21 test suites ran. (13 ms total) 49: [ PASSED ] 151 tests. 49/103 Test #49: OptionsUnitTests .......................... Passed 0.05 sec test 50 Start 50: PbcutilUnitTest 50: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pbcutil/tests 50: Test timeout computed to be: 30 50: [==========] Running 36 tests from 5 test suites. 50: [----------] Global test environment set-up. 50: [----------] 1 test from ShiftTest 50: [ RUN ] ShiftTest.CoordinateShiftWorks 50: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 50: [----------] 1 test from ShiftTest (0 ms total) 50: 50: [----------] 2 tests from MShift 50: [ RUN ] MShift.shiftsAndUnshifts 50: [ OK ] MShift.shiftsAndUnshifts (0 ms) 50: [ RUN ] MShift.shiftsAndUnshiftsSelf 50: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 50: [----------] 2 tests from MShift (0 ms total) 50: 50: [----------] 4 tests from PbcTest 50: [ RUN ] PbcTest.CalcShiftsWorks 50: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 50: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 50: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 50: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 50: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 50: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 50: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 50: [----------] 4 tests from PbcTest (0 ms total) 50: 50: [----------] 2 tests from PbcEnumsTest 50: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 50: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 50: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 50: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 50: [----------] 2 tests from PbcEnumsTest (0 ms total) 50: 50: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 50: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 50: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 50: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (17 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 36 tests from 5 test suites ran. (18 ms total) 50: [ PASSED ] 36 tests. 50/103 Test #50: PbcutilUnitTest ........................... Passed 0.04 sec test 51 Start 51: RandomUnitTests 51: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/random/tests 51: Test timeout computed to be: 30 51: [==========] Running 44 tests from 10 test suites. 51: [----------] Global test environment set-up. 51: [----------] 4 tests from ExponentialDistributionTest 51: [ RUN ] ExponentialDistributionTest.Output 51: [ OK ] ExponentialDistributionTest.Output (0 ms) 51: [ RUN ] ExponentialDistributionTest.Logical 51: [ OK ] ExponentialDistributionTest.Logical (0 ms) 51: [ RUN ] ExponentialDistributionTest.Reset 51: [ OK ] ExponentialDistributionTest.Reset (0 ms) 51: [ RUN ] ExponentialDistributionTest.AltParam 51: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 51: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 51: 51: [----------] 4 tests from GammaDistributionTest 51: [ RUN ] GammaDistributionTest.Output 51: [ OK ] GammaDistributionTest.Output (0 ms) 51: [ RUN ] GammaDistributionTest.Logical 51: [ OK ] GammaDistributionTest.Logical (0 ms) 51: [ RUN ] GammaDistributionTest.Reset 51: [ OK ] GammaDistributionTest.Reset (0 ms) 51: [ RUN ] GammaDistributionTest.AltParam 51: [ OK ] GammaDistributionTest.AltParam (0 ms) 51: [----------] 4 tests from GammaDistributionTest (0 ms total) 51: 51: [----------] 4 tests from NormalDistributionTest 51: [ RUN ] NormalDistributionTest.Output 51: [ OK ] NormalDistributionTest.Output (0 ms) 51: [ RUN ] NormalDistributionTest.Logical 51: [ OK ] NormalDistributionTest.Logical (0 ms) 51: [ RUN ] NormalDistributionTest.Reset 51: [ OK ] NormalDistributionTest.Reset (0 ms) 51: [ RUN ] NormalDistributionTest.AltParam 51: [ OK ] NormalDistributionTest.AltParam (0 ms) 51: [----------] 4 tests from NormalDistributionTest (0 ms total) 51: 51: [----------] 1 test from SeedTest 51: [ RUN ] SeedTest.makeRandomSeed 51: [ OK ] SeedTest.makeRandomSeed (0 ms) 51: [----------] 1 test from SeedTest (0 ms total) 51: 51: [----------] 6 tests from TabulatedNormalDistributionTest 51: [ RUN ] TabulatedNormalDistributionTest.Output14 51: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 51: [ RUN ] TabulatedNormalDistributionTest.Output16 51: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 51: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 51: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 51: [ RUN ] TabulatedNormalDistributionTest.Logical 51: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 51: [ RUN ] TabulatedNormalDistributionTest.Reset 51: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 51: [ RUN ] TabulatedNormalDistributionTest.AltParam 51: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 51: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) 51: 51: [----------] 1 test from TabulatedNormalDistributionTableTest 51: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 51: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 51: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 51: 51: [----------] 6 tests from ThreeFry2x64Test 51: [ RUN ] ThreeFry2x64Test.Logical 51: [ OK ] ThreeFry2x64Test.Logical (0 ms) 51: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 51: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 51: [ RUN ] ThreeFry2x64Test.Reseed 51: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 51: [ RUN ] ThreeFry2x64Test.Discard 51: [ OK ] ThreeFry2x64Test.Discard (0 ms) 51: [ RUN ] ThreeFry2x64Test.InvalidCounter 51: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 51: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 51: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 51: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 51: 51: [----------] 4 tests from UniformIntDistributionTest 51: [ RUN ] UniformIntDistributionTest.Output 51: [ OK ] UniformIntDistributionTest.Output (0 ms) 51: [ RUN ] UniformIntDistributionTest.Logical 51: [ OK ] UniformIntDistributionTest.Logical (0 ms) 51: [ RUN ] UniformIntDistributionTest.Reset 51: [ OK ] UniformIntDistributionTest.Reset (0 ms) 51: [ RUN ] UniformIntDistributionTest.AltParam 51: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 51: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 51: 51: [----------] 5 tests from UniformRealDistributionTest 51: [ RUN ] UniformRealDistributionTest.GenerateCanonical 51: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 51: [ RUN ] UniformRealDistributionTest.Output 51: [ OK ] UniformRealDistributionTest.Output (0 ms) 51: [ RUN ] UniformRealDistributionTest.Logical 51: [ OK ] UniformRealDistributionTest.Logical (0 ms) 51: [ RUN ] UniformRealDistributionTest.Reset 51: [ OK ] UniformRealDistributionTest.Reset (0 ms) 51: [ RUN ] UniformRealDistributionTest.AltParam 51: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 51: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 51: 51: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 51: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 51: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 51: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (3 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 44 tests from 10 test suites ran. (9 ms total) 51: [ PASSED ] 44 tests. 51/103 Test #51: RandomUnitTests ........................... Passed 0.04 sec test 52 Start 52: RestraintTests 52: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/RestraintTests.xml" 52: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/restraint/tests 52: Test timeout computed to be: 30 52: [==========] Running 1 test from 1 test suite. 52: [----------] Global test environment set-up. 52: [----------] 1 test from RestraintManager 52: [ RUN ] RestraintManager.restraintList 52: [ OK ] RestraintManager.restraintList (0 ms) 52: [----------] 1 test from RestraintManager (0 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 1 test from 1 test suite ran. (0 ms total) 52: [ PASSED ] 1 test. 52/103 Test #52: RestraintTests ............................ Passed 0.02 sec test 53 Start 53: SerializationUnitTests 53: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/serialization-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/SerializationUnitTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/serialization/tests 53: Test timeout computed to be: 30 53: [==========] Running 9 tests from 2 test suites. 53: [----------] Global test environment set-up. 53: [----------] 5 tests from InMemorySerializerTest 53: [ RUN ] InMemorySerializerTest.Roundtrip 53: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 53: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 53: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 53: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 53: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 53: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 53: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 53: [ RUN ] InMemorySerializerTest.SizeIsCorrect 53: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 53: [----------] 5 tests from InMemorySerializerTest (0 ms total) 53: 53: [----------] 4 tests from KeyValueTreeSerializerTest 53: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 53: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 53: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 53: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 53: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 53: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 53: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 53: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 53: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 9 tests from 2 test suites ran. (2 ms total) 53: [ PASSED ] 9 tests. 53/103 Test #53: SerializationUnitTests .................... Passed 0.03 sec test 54 Start 54: TableUnitTests 54: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tables/tests 54: Test timeout computed to be: 30 54: [==========] Running 16 tests from 2 test suites. 54: [----------] Global test environment set-up. 54: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 54: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 54: [ OK ] SplineTableTest/0.HandlesIncorrectInput (1 ms) 54: [ RUN ] SplineTableTest/0.Sinc 54: [ OK ] SplineTableTest/0.Sinc (0 ms) 54: [ RUN ] SplineTableTest/0.LJ12 54: [ OK ] SplineTableTest/0.LJ12 (15 ms) 54: [ RUN ] SplineTableTest/0.PmeCorrection 54: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 54: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 54: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 54: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 54: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 54: [ RUN ] SplineTableTest/0.TwoFunctions 54: [ OK ] SplineTableTest/0.TwoFunctions (27 ms) 54: [ RUN ] SplineTableTest/0.ThreeFunctions 54: [ OK ] SplineTableTest/0.ThreeFunctions (33 ms) 54: [----------] 8 tests from SplineTableTest/0 (82 ms total) 54: 54: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 54: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 54: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 54: [ RUN ] SplineTableTest/1.Sinc 54: [ OK ] SplineTableTest/1.Sinc (1 ms) 54: [ RUN ] SplineTableTest/1.LJ12 54: [ OK ] SplineTableTest/1.LJ12 (36 ms) 54: [ RUN ] SplineTableTest/1.PmeCorrection 54: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 54: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 54: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 54: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 54: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (1 ms) 54: [ RUN ] SplineTableTest/1.TwoFunctions 54: [ OK ] SplineTableTest/1.TwoFunctions (79 ms) 54: [ RUN ] SplineTableTest/1.ThreeFunctions 54: [ OK ] SplineTableTest/1.ThreeFunctions (89 ms) 54: [----------] 8 tests from SplineTableTest/1 (212 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 16 tests from 2 test suites ran. (295 ms total) 54: [ PASSED ] 16 tests. 54/103 Test #54: TableUnitTests ............................ Passed 0.32 sec test 55 Start 55: TaskAssignmentUnitTests 55: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/taskassignment/tests 55: Test timeout computed to be: 30 55: [==========] Running 3 tests from 2 test suites. 55: [----------] Global test environment set-up. 55: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 55: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 55: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 55: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 55: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 55: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 55: 55: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 55: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 55: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 55: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 3 tests from 2 test suites ran. (1 ms total) 55: [ PASSED ] 3 tests. 55/103 Test #55: TaskAssignmentUnitTests ................... Passed 0.03 sec test 56 Start 56: GmxTimingTests 56: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/timing/tests 56: Test timeout computed to be: 30 56: [==========] Running 6 tests from 1 test suite. 56: [----------] Global test environment set-up. 56: [----------] 6 tests from TimingTest 56: [ RUN ] TimingTest.ElementCountingWorks 56: [ OK ] TimingTest.ElementCountingWorks (0 ms) 56: [ RUN ] TimingTest.ElementNoCountingWorks 56: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 56: [ RUN ] TimingTest.SubElementCountingWorks 56: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 56: [ RUN ] TimingTest.SubElementNoCountingWorks 56: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 56: [ RUN ] TimingTest.RunWallCycle 56: [ OK ] TimingTest.RunWallCycle (1 ms) 56: [ RUN ] TimingTest.RunWallCycleSub 56: [ OK ] TimingTest.RunWallCycleSub (0 ms) 56: [----------] 6 tests from TimingTest (1 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 6 tests from 1 test suite ran. (1 ms total) 56: [ PASSED ] 6 tests. 56/103 Test #56: GmxTimingTests ............................ Passed 0.03 sec test 57 Start 57: TopologyTest 57: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/TopologyTest.xml" 57: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/topology/tests 57: Test timeout computed to be: 30 57: [==========] Running 153 tests from 10 test suites. 57: [----------] Global test environment set-up. 57: [----------] 3 tests from PdbAtomEntryTest 57: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 57: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 57: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 57: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 57: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 57: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 57: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 57: 57: [----------] 3 tests from ExclusionBlockTest 57: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 57: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 57: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 57: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 57: [ RUN ] ExclusionBlockTest.MergeExclusions 57: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 57: [----------] 3 tests from ExclusionBlockTest (0 ms total) 57: 57: [----------] 6 tests from InteractionListTest 57: [ RUN ] InteractionListTest.EmptyWorks 57: [ OK ] InteractionListTest.EmptyWorks (0 ms) 57: [ RUN ] InteractionListTest.CanAddInteractionArray 57: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 57: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 57: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 57: [ RUN ] InteractionListTest.CanAddInteractionPointer 57: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 57: [ RUN ] InteractionListTest.CanAddListToOtherList 57: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 57: [ RUN ] InteractionListTest.ClearingWorks 57: [ OK ] InteractionListTest.ClearingWorks (0 ms) 57: [----------] 6 tests from InteractionListTest (0 ms total) 57: 57: [----------] 3 tests from IndexTest 57: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: The atomic radii are set according to: 57: 57: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 57: A. Bondi 57: van der Waals Volumes and Radii 57: J. Phys. Chem. (1964) 57: https://doi.org/10.1021/j100785a001 57: -------- -------- --- Thank You --- -------- -------- 57: 57: [ OK ] IndexTest.AnalyseWorksDefaultGroups (7 ms) 57: [ RUN ] IndexTest.WriteIndexWorks 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: The atomic radii are set according to: 57: 57: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 57: A. Bondi 57: van der Waals Volumes and Radii 57: J. Phys. Chem. (1964) 57: https://doi.org/10.1021/j100785a001 57: -------- -------- --- Thank You --- -------- -------- 57: 57: [ OK ] IndexTest.WriteIndexWorks (33 ms) 57: [ RUN ] IndexTest.WriteAndReadIndexWorks 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: The atomic radii are set according to: 57: 57: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 57: A. Bondi 57: van der Waals Volumes and Radii 57: J. Phys. Chem. (1964) 57: https://doi.org/10.1021/j100785a001 57: -------- -------- --- Thank You --- -------- -------- 57: 57: [ OK ] IndexTest.WriteAndReadIndexWorks (5 ms) 57: [----------] 3 tests from IndexTest (46 ms total) 57: 57: [----------] 4 tests from MtopTest 57: [ RUN ] MtopTest.RangeBasedLoop 57: [ OK ] MtopTest.RangeBasedLoop (0 ms) 57: [ RUN ] MtopTest.Operators 57: [ OK ] MtopTest.Operators (0 ms) 57: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 57: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 57: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 57: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 57: [----------] 4 tests from MtopTest (0 ms total) 57: 57: [----------] 2 tests from IListRangeTest 57: [ RUN ] IListRangeTest.RangeBasedLoopWorks 57: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 57: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 57: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 57: [----------] 2 tests from IListRangeTest (0 ms total) 57: 57: [----------] 13 tests from StringTableTest 57: [ RUN ] StringTableTest.AddSingleEntry 57: [ OK ] StringTableTest.AddSingleEntry (0 ms) 57: [ RUN ] StringTableTest.CanAccessWithAt 57: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 57: [ RUN ] StringTableTest.CanAccessWithBracket 57: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 57: [ RUN ] StringTableTest.ThrowsOutOfRange 57: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 57: [ RUN ] StringTableTest.StringCompareIsCorrect 57: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 57: [ RUN ] StringTableTest.AddTwoDistinctEntries 57: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 57: [ RUN ] StringTableTest.TryToAddDuplicates 57: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 57: [ RUN ] StringTableTest.AddLargeNumberOfEntries 57: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 57: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 57: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 57: [ RUN ] StringTableTest.CanWriteToBuffer 57: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 57: [ RUN ] StringTableTest.Roundtrip 57: [ OK ] StringTableTest.Roundtrip (0 ms) 57: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 57: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 57: [ RUN ] StringTableTest.CanCopyToLegacyTable 57: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 57: [----------] 13 tests from StringTableTest (4 ms total) 57: 57: [----------] 6 tests from LegacySymtabTest 57: [ RUN ] LegacySymtabTest.EmptyOnOpen 57: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 57: [ RUN ] LegacySymtabTest.AddSingleEntry 57: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 57: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 57: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 57: [ RUN ] LegacySymtabTest.TryToAddDuplicates 57: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 57: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 57: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 57: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 57: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 57: [----------] 6 tests from LegacySymtabTest (0 ms total) 57: 57: [----------] 5 tests from TopSortTest 57: [ RUN ] TopSortTest.WorksOnEmptyIdef 57: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 57: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 57: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 57: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 57: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 57: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 57: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 57: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 57: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 57: [----------] 5 tests from TopSortTest (0 ms total) 57: 57: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 57: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 57: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 57: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (34 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 153 tests from 10 test suites ran. (87 ms total) 57: [ PASSED ] 153 tests. 57: 57: YOU HAVE 1 DISABLED TEST 57: 57/103 Test #57: TopologyTest .............................. Passed 0.12 sec test 58 Start 58: PullTest 58: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/PullTest.xml" 58: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/pulling/tests 58: Test timeout computed to be: 30 58: [==========] Running 10 tests from 1 test suite. 58: [----------] Global test environment set-up. 58: [----------] 10 tests from PullTest 58: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 58: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 58: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 58: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 58: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 58: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 58: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 58: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 58: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 58: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 58: [ RUN ] PullTest.TransformationCoordSimple 58: [ OK ] PullTest.TransformationCoordSimple (0 ms) 58: [ RUN ] PullTest.TransformationCoordAdvanced 58: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 58: [ RUN ] PullTest.TransformationCoordTime 58: [ OK ] PullTest.TransformationCoordTime (0 ms) 58: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 58: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 58: [ RUN ] PullTest.TransformationCoordDummyExpression 58: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 58: [----------] 10 tests from PullTest (1 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 10 tests from 1 test suite ran. (1 ms total) 58: [ PASSED ] 10 tests. 58/103 Test #58: PullTest .................................. Passed 0.03 sec test 59 Start 59: SimdUnitTests 59: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/simd/tests 59: Test timeout computed to be: 30 59: [==========] Running 86 tests from 3 test suites. 59: [----------] Global test environment set-up. 59: [----------] 41 tests from SimdScalarTest 59: [ RUN ] SimdScalarTest.load 59: [ OK ] SimdScalarTest.load (0 ms) 59: [ RUN ] SimdScalarTest.loadU 59: [ OK ] SimdScalarTest.loadU (0 ms) 59: [ RUN ] SimdScalarTest.store 59: [ OK ] SimdScalarTest.store (0 ms) 59: [ RUN ] SimdScalarTest.storeU 59: [ OK ] SimdScalarTest.storeU (0 ms) 59: [ RUN ] SimdScalarTest.setZero 59: [ OK ] SimdScalarTest.setZero (0 ms) 59: [ RUN ] SimdScalarTest.andNot 59: [ OK ] SimdScalarTest.andNot (0 ms) 59: [ RUN ] SimdScalarTest.fma 59: [ OK ] SimdScalarTest.fma (0 ms) 59: [ RUN ] SimdScalarTest.fms 59: [ OK ] SimdScalarTest.fms (0 ms) 59: [ RUN ] SimdScalarTest.fnma 59: [ OK ] SimdScalarTest.fnma (0 ms) 59: [ RUN ] SimdScalarTest.fnms 59: [ OK ] SimdScalarTest.fnms (0 ms) 59: [ RUN ] SimdScalarTest.maskAdd 59: [ OK ] SimdScalarTest.maskAdd (0 ms) 59: [ RUN ] SimdScalarTest.maskzMul 59: [ OK ] SimdScalarTest.maskzMul (0 ms) 59: [ RUN ] SimdScalarTest.maskzFma 59: [ OK ] SimdScalarTest.maskzFma (0 ms) 59: [ RUN ] SimdScalarTest.abs 59: [ OK ] SimdScalarTest.abs (0 ms) 59: [ RUN ] SimdScalarTest.max 59: [ OK ] SimdScalarTest.max (0 ms) 59: [ RUN ] SimdScalarTest.min 59: [ OK ] SimdScalarTest.min (0 ms) 59: [ RUN ] SimdScalarTest.round 59: [ OK ] SimdScalarTest.round (0 ms) 59: [ RUN ] SimdScalarTest.trunc 59: [ OK ] SimdScalarTest.trunc (0 ms) 59: [ RUN ] SimdScalarTest.reduce 59: [ OK ] SimdScalarTest.reduce (0 ms) 59: [ RUN ] SimdScalarTest.testBits 59: [ OK ] SimdScalarTest.testBits (0 ms) 59: [ RUN ] SimdScalarTest.anyTrue 59: [ OK ] SimdScalarTest.anyTrue (0 ms) 59: [ RUN ] SimdScalarTest.selectByMask 59: [ OK ] SimdScalarTest.selectByMask (0 ms) 59: [ RUN ] SimdScalarTest.selectByNotMask 59: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 59: [ RUN ] SimdScalarTest.blend 59: [ OK ] SimdScalarTest.blend (0 ms) 59: [ RUN ] SimdScalarTest.cvtR2I 59: [ OK ] SimdScalarTest.cvtR2I (0 ms) 59: [ RUN ] SimdScalarTest.cvttR2I 59: [ OK ] SimdScalarTest.cvttR2I (0 ms) 59: [ RUN ] SimdScalarTest.cvtI2R 59: [ OK ] SimdScalarTest.cvtI2R (0 ms) 59: [ RUN ] SimdScalarTest.cvtF2D 59: [ OK ] SimdScalarTest.cvtF2D (0 ms) 59: [ RUN ] SimdScalarTest.cvtD2D 59: [ OK ] SimdScalarTest.cvtD2D (0 ms) 59: [ RUN ] SimdScalarTest.loadI 59: [ OK ] SimdScalarTest.loadI (0 ms) 59: [ RUN ] SimdScalarTest.loadUI 59: [ OK ] SimdScalarTest.loadUI (0 ms) 59: [ RUN ] SimdScalarTest.storeI 59: [ OK ] SimdScalarTest.storeI (0 ms) 59: [ RUN ] SimdScalarTest.storeUI 59: [ OK ] SimdScalarTest.storeUI (0 ms) 59: [ RUN ] SimdScalarTest.andNotI 59: [ OK ] SimdScalarTest.andNotI (0 ms) 59: [ RUN ] SimdScalarTest.testBitsI 59: [ OK ] SimdScalarTest.testBitsI (0 ms) 59: [ RUN ] SimdScalarTest.selectByMaskI 59: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 59: [ RUN ] SimdScalarTest.selectByNotMaskI 59: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 59: [ RUN ] SimdScalarTest.blendI 59: [ OK ] SimdScalarTest.blendI (0 ms) 59: [ RUN ] SimdScalarTest.cvtB2IB 59: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 59: [ RUN ] SimdScalarTest.cvtIB2B 59: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 59: [ RUN ] SimdScalarTest.expandScalarsToTriplets 59: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 59: [----------] 41 tests from SimdScalarTest (0 ms total) 59: 59: [----------] 8 tests from SimdScalarUtilTest 59: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 59: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 59: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 59: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 59: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 59: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 59: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 59: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 59: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 59: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 59: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 59: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 59: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 59: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 59: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 59: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 59: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 59: 59: [----------] 37 tests from SimdScalarMathTest 59: [ RUN ] SimdScalarMathTest.copysign 59: [ OK ] SimdScalarMathTest.copysign (0 ms) 59: [ RUN ] SimdScalarMathTest.invsqrtPair 59: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 59: [ RUN ] SimdScalarMathTest.inv 59: [ OK ] SimdScalarMathTest.inv (0 ms) 59: [ RUN ] SimdScalarMathTest.maskzInvsqrt 59: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 59: [ RUN ] SimdScalarMathTest.log 59: [ OK ] SimdScalarMathTest.log (0 ms) 59: [ RUN ] SimdScalarMathTest.exp2 59: [ OK ] SimdScalarMathTest.exp2 (0 ms) 59: [ RUN ] SimdScalarMathTest.exp 59: [ OK ] SimdScalarMathTest.exp (0 ms) 59: [ RUN ] SimdScalarMathTest.erf 59: [ OK ] SimdScalarMathTest.erf (0 ms) 59: [ RUN ] SimdScalarMathTest.erfc 59: [ OK ] SimdScalarMathTest.erfc (0 ms) 59: [ RUN ] SimdScalarMathTest.sincos 59: [ OK ] SimdScalarMathTest.sincos (0 ms) 59: [ RUN ] SimdScalarMathTest.sin 59: [ OK ] SimdScalarMathTest.sin (0 ms) 59: [ RUN ] SimdScalarMathTest.cos 59: [ OK ] SimdScalarMathTest.cos (0 ms) 59: [ RUN ] SimdScalarMathTest.tan 59: [ OK ] SimdScalarMathTest.tan (0 ms) 59: [ RUN ] SimdScalarMathTest.asin 59: [ OK ] SimdScalarMathTest.asin (0 ms) 59: [ RUN ] SimdScalarMathTest.acos 59: [ OK ] SimdScalarMathTest.acos (0 ms) 59: [ RUN ] SimdScalarMathTest.atan 59: [ OK ] SimdScalarMathTest.atan (0 ms) 59: [ RUN ] SimdScalarMathTest.atan2 59: [ OK ] SimdScalarMathTest.atan2 (0 ms) 59: [ RUN ] SimdScalarMathTest.pmeForceCorrection 59: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 59: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 59: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 59: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 59: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.invSingleAccuracy 59: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 59: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.logSingleAccuracy 59: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 59: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.expSingleAccuracy 59: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 59: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 59: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 59: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 59: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 59: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 59: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 59: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 59: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 59: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 59: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 59: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 59: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 59: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 59: [----------] 37 tests from SimdScalarMathTest (0 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 86 tests from 3 test suites ran. (0 ms total) 59: [ PASSED ] 86 tests. 59/103 Test #59: SimdUnitTests ............................. Passed 0.03 sec test 60 Start 60: CompatibilityHelpersTests 60: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/compat/tests 60: Test timeout computed to be: 30 60: [==========] Running 9 tests from 6 test suites. 60: [----------] Global test environment set-up. 60: [----------] 4 tests from TemplateMPTest 60: [ RUN ] TemplateMPTest.MpWithIndexInt 60: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 60: [ RUN ] TemplateMPTest.MpWithIndexIntBad 60: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 60: [ RUN ] TemplateMPTest.MpWithIndexBool 60: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 60: [ RUN ] TemplateMPTest.MpWithIndexEnum 60: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 60: [----------] 4 tests from TemplateMPTest (0 ms total) 60: 60: [----------] 1 test from NotNullConstruction 60: [ RUN ] NotNullConstruction.Works 60: [ OK ] NotNullConstruction.Works (0 ms) 60: [----------] 1 test from NotNullConstruction (0 ms total) 60: 60: [----------] 1 test from NotNullCasting 60: [ RUN ] NotNullCasting.Works 60: [ OK ] NotNullCasting.Works (0 ms) 60: [----------] 1 test from NotNullCasting (0 ms total) 60: 60: [----------] 1 test from NotNullAssignment 60: [ RUN ] NotNullAssignment.Works 60: [ OK ] NotNullAssignment.Works (0 ms) 60: [----------] 1 test from NotNullAssignment (0 ms total) 60: 60: [----------] 1 test from MakeNotNull 60: [ RUN ] MakeNotNull.Works 60: [ OK ] MakeNotNull.Works (0 ms) 60: [----------] 1 test from MakeNotNull (0 ms total) 60: 60: [----------] 1 test from NotNull 60: [ RUN ] NotNull.WorksInContainers 60: [ OK ] NotNull.WorksInContainers (0 ms) 60: [----------] 1 test from NotNull (0 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 9 tests from 6 test suites ran. (0 ms total) 60: [ PASSED ] 9 tests. 60/103 Test #60: CompatibilityHelpersTests ................. Passed 0.02 sec test 61 Start 61: GmxAnaTest 61: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 61: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests 61: Test timeout computed to be: 600 61: [==========] Running 37 tests from 10 test suites. 61: [----------] Global test environment set-up. 61: [----------] 7 tests from Entropy 61: [ RUN ] Entropy.Schlitter_300_NoLinear 61: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 61: [ RUN ] Entropy.Schlitter_300_Linear 61: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 61: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 61: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 61: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 61: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 61: [ RUN ] Entropy.QuasiHarmonic_200_Linear 61: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 61: [ RUN ] Entropy.EntropyCompare_200_Linear 61: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 61: [ RUN ] Entropy.EntropyCompare_300_Linear 61: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 61: [----------] 7 tests from Entropy (2 ms total) 61: 61: [----------] 2 tests from GmxChiTest 61: [ RUN ] GmxChiTest.gmxchiWorksWithAll 61: Analyzing from residue 1 to residue 11 61: 10 residues with dihedrals found 61: 46 dihedrals found 61: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 61: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 61: j after resetting (nr. active dihedrals) = 46 61: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 61: Now calculating transitions... 61: Total number of transitions: 0 61: Now printing out transitions and OPs... 61: Now printing out rotamer occupancies... 61: Now calculating Chi product trajectories... 61: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 61: [ OK ] GmxChiTest.gmxchiWorksWithAll (1710 ms) 61: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 61: Analyzing from residue 2 to residue 6 61: 5 residues with dihedrals found 61: 23 dihedrals found 61: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 61: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 61: j after resetting (nr. active dihedrals) = 23 61: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 61: Now calculating transitions... 61: Total number of transitions: 0 61: Now printing out transitions and OPs... 61: Now printing out rotamer occupancies... 61: Now calculating Chi product trajectories... 61: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 61: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (901 ms) 61: [----------] 2 tests from GmxChiTest (3055 ms total) 61: 61: [----------] 10 tests from MindistTest 61: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 0: 'atom1' 61: Selected 1: 'atom2' 61: [ OK ] MindistTest.mindistWorksWithSingleAtoms (57 ms) 61: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 2: 'atom3' 61: Selected 3: 'atoms12' 61: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (1 ms) 61: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 0: 'atom1' 61: Selected 1: 'atom2' 61: [ OK ] MindistTest.mindistDoesNotPickUpContacts (1 ms) 61: [ RUN ] MindistTest.mindistPicksUpContacts 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 0: 'atom1' 61: Selected 1: 'atom2' 61: [ OK ] MindistTest.mindistPicksUpContacts (1 ms) 61: [ RUN ] MindistTest.ngWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 0: 'atom1' 61: Selected 1: 'atom2' 61: Selected 2: 'atom3' 61: [ OK ] MindistTest.ngWorks (1 ms) 61: [ RUN ] MindistTest.groupWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 3: 'atoms12' 61: Selected 2: 'atom3' 61: [ OK ] MindistTest.groupWorks (1 ms) 61: [ RUN ] MindistTest.maxDistWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 2: 'atom3' 61: Selected 3: 'atoms12' 61: [ OK ] MindistTest.maxDistWorks (1 ms) 61: [ RUN ] MindistTest.noPbcWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 0: 'atom1' 61: Selected 1: 'atom2' 61: [ OK ] MindistTest.noPbcWorks (1 ms) 61: [ RUN ] MindistTest.resPerTimeWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 3: 'atoms12' 61: Selected 2: 'atom3' 61: [ OK ] MindistTest.resPerTimeWorks (1 ms) 61: [ RUN ] MindistTest.matrixWorks 61: Group 0 ( atom1) has 1 elements 61: Group 1 ( atom2) has 1 elements 61: Group 2 ( atom3) has 1 elements 61: Group 3 ( atoms12) has 2 elements 61: Group 4 ( atoms23) has 2 elements 61: Group 5 ( atoms123) has 3 elements 61: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Selected 5: 'atoms123' 61: Special case: making distance matrix between all atoms in group atoms123 61: [ OK ] MindistTest.matrixWorks (1 ms) 61: [----------] 10 tests from MindistTest (71 ms total) 61: 61: [----------] 1 test from GmxRmsTest 61: [ RUN ] GmxRmsTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Select group for least squares fit 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Select group for RMSD calculation 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 61: Setting the LD random seed to -270352397 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 1: 'Protein' 61: Selected 1: 'Protein' 61: [ OK ] GmxRmsTest.BasicOutputWorks (1039 ms) 61: [----------] 1 test from GmxRmsTest (1039 ms total) 61: 61: [----------] 1 test from GmxRmsdistTest 61: [ RUN ] GmxRmsdistTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsdistTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 61: 61: rmsmax = 0.382568, rmscmax = 0.659498 61: Setting the LD random seed to -67408524 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 0: 'System' 61: [ OK ] GmxRmsdistTest.BasicOutputWorks (1001 ms) 61: [----------] 1 test from GmxRmsdistTest (1001 ms total) 61: 61: [----------] 1 test from GmxRmsfTest 61: [ RUN ] GmxRmsfTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRmsfTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Select group(s) for root mean square calculation 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Last frame 2 time 2.000 61: Setting the LD random seed to 1959919603 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 3: 'C-alpha' 61: [ OK ] GmxRmsfTest.BasicOutputWorks (990 ms) 61: [----------] 1 test from GmxRmsfTest (990 ms total) 61: 61: [----------] 1 test from GmxSorientTest 61: [ RUN ] GmxSorientTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 1818.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSorientTest_BasicOutputWorks_alanine_vsite_solvated.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Group 0 ( System) has 923 elements 61: Group 1 ( Protein) has 29 elements 61: Group 2 ( Protein-H) has 17 elements 61: Group 3 ( C-alpha) has 2 elements 61: Group 4 ( Backbone) has 6 elements 61: Group 5 ( MainChain) has 9 elements 61: Group 6 ( MainChain+Cb) has 11 elements 61: Group 7 ( MainChain+H) has 13 elements 61: Group 8 ( SideChain) has 16 elements 61: Group 9 ( SideChain-H) has 8 elements 61: Group 10 ( Prot-Masses) has 23 elements 61: Group 11 ( non-Protein) has 894 elements 61: Group 12 ( Water) has 894 elements 61: Group 13 ( SOL) has 894 elements 61: Group 14 ( non-Water) has 29 elements 61: Select a group: Select a group: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: Average nr of molecules between 0 and 0.5 nm: 13.0 61: Average cos(theta1) between 0 and 0.5 nm: 0.103 61: Average 3cos2(theta2)-1 between 0 and 0.5 nm: -0.098 61: Setting the LD random seed to 2012462806 61: 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.pdb', all velocities are zero 61: 61: Cleaning up constraints and constant bonded interactions with virtual sites 61: 61: Converted 15 Bonds with virtual sites to connections, 7 left 61: 61: Removed 18 Angles with virtual sites, 21 left 61: 61: Removed 10 Proper Dih.s with virtual sites, 44 left 61: Analysing residue names: 61: There are: 2 Protein residues 61: There are: 298 Water residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Select a group of reference particles and a solvent group: 61: Selected 1: 'Protein' 61: Selected 12: 'Water' 61: [ OK ] GmxSorientTest.BasicOutputWorks (63 ms) 61: [----------] 1 test from GmxSorientTest (63 ms total) 61: 61: [----------] 1 test from GmxRotmatTest 61: [ RUN ] GmxRotmatTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 2 [file lysozyme.top, line 1465]: 61: System has non-zero total charge: 2.000000 61: Total charge should normally be an integer. See 61: https://manual.gromacs.org/current/user-guide/floating-point.html 61: for discussion on how close it should be to an integer. 61: 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 465.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxRotmatTest_BasicOutputWorks_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Group 0 ( System) has 156 elements 61: Group 1 ( Protein) has 156 elements 61: Group 2 ( Protein-H) has 75 elements 61: Group 3 ( C-alpha) has 10 elements 61: Group 4 ( Backbone) has 30 elements 61: Group 5 ( MainChain) has 40 elements 61: Group 6 ( MainChain+Cb) has 49 elements 61: Group 7 ( MainChain+H) has 52 elements 61: Group 8 ( SideChain) has 104 elements 61: Group 9 ( SideChain-H) has 35 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Setting the LD random seed to -1082137113 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 10 Protein residues 61: Analysing Protein... 61: 61: This run will generate roughly 0 Mb of data 61: Selected 4: 'Backbone' 61: [ OK ] GmxRotmatTest.BasicOutputWorks (990 ms) 61: [----------] 1 test from GmxRotmatTest (990 ms total) 61: 61: [----------] 1 test from GmxSaltbrTest 61: [ RUN ] GmxSaltbrTest.BasicOutputWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 3 NOTEs 61: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/GmxSaltbrTest_BasicOutputWorks_spc2-traj.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 61: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: 61: Setting the LD random seed to 1568571199 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb', all velocities are zero 61: Analysing residue names: 61: There are: 2 Water residues 61: 61: This run will generate roughly 0 Mb of data 61: CG: SOL1-1 Q: -0.834 Atoms: 0 61: CG: SOL1-2 Q: 0.417 Atoms: 1 61: CG: SOL1-3 Q: 0.417 Atoms: 2 61: CG: SOL2-4 Q: -0.834 Atoms: 3 61: CG: SOL2-5 Q: 0.417 Atoms: 4 61: CG: SOL2-6 Q: 0.417 Atoms: 5 61: [ OK ] GmxSaltbrTest.BasicOutputWorks (10 ms) 61: [----------] 1 test from GmxSaltbrTest (10 ms total) 61: 61: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: trr version: GMX_trn_file (single precision) 61: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (2 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (1 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 61: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (2 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (2 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (2 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (23 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (4 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (4 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 61: Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (4 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (3 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (3 ms) 61: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 61: 61: WARNING: Masses and atomic (Van der Waals) radii will be guessed 61: based on residue and atom names, since they could not be 61: definitively assigned from the information in your input 61: files. These guessed numbers might deviate from the mass 61: and radius of the atom type. Please check the output 61: files if necessary. Note, that this functionality may 61: be removed in a future GROMACS version. Please, consider 61: using another file format for your input. 61: 61: The atomic radii are set according to: 61: 61: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 61: A. Bondi 61: van der Waals Volumes and Radii 61: J. Phys. Chem. (1964) 61: https://doi.org/10.1021/j100785a001 61: -------- -------- --- Thank You --- -------- -------- 61: 61: Group 0 ( System) has 6 elements 61: Group 1 ( Water) has 6 elements 61: Group 2 ( SOL) has 6 elements 61: Select a group: Reading frame 0 time 0.000 61: WARNING: If there are molecules in the input trajectory file 61: that are broken across periodic boundaries, they 61: cannot be made whole (or treated as whole) without 61: you providing a run input file. 61: 61: Reading frame 1 time 1.000 Last frame 1 time 1.000 61: Selected 0: 'System' 61: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (3 ms) 61: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (59 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 37 tests from 10 test suites ran. (7286 ms total) 61: [ PASSED ] 37 tests. 61/103 Test #61: GmxAnaTest ................................ Passed 7.33 sec test 62 Start 62: GmxPreprocessTests 62: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests 62: Test timeout computed to be: 1920 62: [==========] Running 237 tests from 16 test suites. 62: [----------] Global test environment set-up. 62: [----------] 1 test from ConvertInteractionsTest 62: [ RUN ] ConvertInteractionsTest.DoingNothingWorks 62: [ OK ] ConvertInteractionsTest.DoingNothingWorks (0 ms) 62: [----------] 1 test from ConvertInteractionsTest (0 ms total) 62: 62: [----------] 5 tests from GenconfTest 62: [ RUN ] GenconfTest.nbox_Works 62: [ OK ] GenconfTest.nbox_Works (1 ms) 62: [ RUN ] GenconfTest.nbox_norenumber_Works 62: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms) 62: [ RUN ] GenconfTest.nbox_dist_Works 62: [ OK ] GenconfTest.nbox_dist_Works (1 ms) 62: [ RUN ] GenconfTest.nbox_rot_Works 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: center of geometry: 1.733667, 1.477000, 0.905167 62: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 62: [ RUN ] GenconfTest.trj_Works 62: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 62: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Last frame 3 time 3.000 62: [ OK ] GenconfTest.trj_Works (1 ms) 62: [----------] 5 tests from GenconfTest (7 ms total) 62: 62: [----------] 2 tests from GenionTest 62: [ RUN ] GenionTest.HighConcentrationIonPlacement 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 62: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 62: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 62: on the accuracy of your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 62: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 62: buffer. The cluster pair list does have a buffering effect, but choosing 62: a larger rlist might be necessary for good energy conservation. 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 62: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 62: < 0 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 1308.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Group 0 ( System) has 653 elements 62: Group 1 ( Water) has 648 elements 62: Group 2 ( SOL) has 648 elements 62: Group 3 ( non-Water) has 5 elements 62: Group 4 ( Other) has 5 elements 62: Group 5 ( METH) has 5 elements 62: Select a group: Number of (3-atomic) solvent molecules: 216 62: Using random seed 1997. 62: Replacing solvent molecule 56 (atom 168) with NA 62: Replacing solvent molecule 120 (atom 360) with NA 62: Replacing solvent molecule 182 (atom 546) with NA 62: Replacing solvent molecule 71 (atom 213) with NA 62: Replacing solvent molecule 189 (atom 567) with CL 62: Replacing solvent molecule 54 (atom 162) with CL 62: Replacing solvent molecule 155 (atom 465) with CL 62: Replacing solvent molecule 99 (atom 297) with CL 62: 62: Setting the LD random seed to -814224981 62: 62: Generated 331705 of the 331705 non-bonded parameter combinations 62: 62: Generated 331705 of the 331705 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Excluding 3 bonded neighbours molecule type 'methane' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216_with_methane.gro' 62: Analysing residue names: 62: There are: 216 Water residues 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: This run will generate roughly 0 Mb of data 62: Will try to add 4 NA ions and 4 CL ions. 62: Select a continuous group of solvent molecules 62: Selected 1: 'Water' 62: [ OK ] GenionTest.HighConcentrationIonPlacement (1004 ms) 62: [ RUN ] GenionTest.NoIonPlacement 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 62: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 62: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 62: on the accuracy of your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 62: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 62: buffer. The cluster pair list does have a buffering effect, but choosing 62: a larger rlist might be necessary for good energy conservation. 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 62: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 62: < 0 62: 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 1308.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: No ions to add, will just copy input configuration. 62: Setting the LD random seed to 1983905521 62: 62: Generated 331705 of the 331705 non-bonded parameter combinations 62: 62: Generated 331705 of the 331705 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Excluding 3 bonded neighbours molecule type 'methane' 62: 62: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216_with_methane.gro' 62: Analysing residue names: 62: There are: 216 Water residues 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] GenionTest.NoIonPlacement (988 ms) 62: [----------] 2 tests from GenionTest (1993 ms total) 62: 62: [----------] 1 test from GenRestrTest 62: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 62: 62: Reading structure file 62: Group 0 ( System) has 156 elements 62: Group 1 ( Protein) has 156 elements 62: Group 2 ( Protein-H) has 75 elements 62: Group 3 ( C-alpha) has 10 elements 62: Group 4 ( Backbone) has 30 elements 62: Group 5 ( MainChain) has 40 elements 62: Group 6 ( MainChain+Cb) has 49 elements 62: Group 7 ( MainChain+H) has 52 elements 62: Group 8 ( SideChain) has 104 elements 62: Group 9 ( SideChain-H) has 35 elements 62: Select a group: Select group to position restrain 62: Selected 3: 'C-alpha' 62: [ OK ] GenRestrTest.SimpleRestraintsGenerated (3 ms) 62: [----------] 1 test from GenRestrTest (3 ms total) 62: 62: [----------] 9 tests from PreprocessingAtomTypesTest 62: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 62: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 62: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 62: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 62: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 62: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 62: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 62: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 62: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 62: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 62: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 62: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 62: 62: [----------] 10 tests from PreprocessingBondAtomTypeTest 62: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 62: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 62: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 62: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 62: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 62: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 62: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 62: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 62: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 62: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 62: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 62: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 62: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 62: 62: [----------] 3 tests from GromppDirectiveTest 62: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -137398858 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1145373546 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (9 ms) 62: [ RUN ] GromppDirectiveTest.NoteOnDihedralNotSumToZero 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: 1 dihedrals with function type 3 (Ryckaert-Bellemans or Fourier) have 62: coefficients that do not sum to zero. This does not affect the simulation 62: and can be ignored, unless you are comparing potential energy values with 62: other force field ports and/or MD software. 62: First such dihedral in molecule A, involving atoms 0 2 1 3 62: 62: 62: NOTE 2 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_NoteOnDihedralNotSumToZero_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 3 NOTEs 62: Setting the LD random seed to -1615331347 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -21567554 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] GromppDirectiveTest.NoteOnDihedralNotSumToZero (31 ms) 62: [ RUN ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy 62: Setting the LD random seed to -4393570 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -257069106 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] GromppDirectiveTest.WarnOnDihedralSumDifferentForFreeEnergy (15 ms) 62: [----------] 3 tests from GromppDirectiveTest (56 ms total) 62: 62: [----------] 6 tests from InsertMoleculesTest 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 62: Reading solute configuration 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Try 1 success (now 8 atoms)! 62: 62: Added 1 molecules (out of 1 requested) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 62: 62: Output configuration contains 8 atoms in 4 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (10 ms) 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Try 1 success (now 2 atoms)! 62: Try 2 success (now 4 atoms)! 62: Try 3 success (now 6 atoms)! 62: Try 4 success (now 8 atoms)! 62: Try 5 success (now 10 atoms)! 62: 62: Added 5 molecules (out of 5 requested) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 62: 62: Output configuration contains 10 atoms in 10 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (2 ms) 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Try 1 success (now 2 atoms)! 62: Try 2 success (now 4 atoms)! 62: Try 3 success (now 6 atoms)! 62: Try 4 success (now 8 atoms)! 62: Try 5 success (now 10 atoms)! 62: 62: Added 5 molecules (out of 5 requested) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBoxConcentration_out.gro 62: 62: Output configuration contains 10 atoms in 10 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBoxConcentration (2 ms) 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 62: Reading solute configuration 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Try 1 success (now 8 atoms)! 62: Try 2 success (now 10 atoms)! 62: 62: Added 2 molecules (out of 2 requested) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 62: 62: Output configuration contains 10 atoms in 4 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (2 ms) 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 62: Reading solute configuration 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Try 1 success (now 650 atoms)! 62: Try 2 success (now 652 atoms)! 62: Try 3 success (now 654 atoms)! 62: Try 4 success (now 656 atoms)! 62: 62: Added 4 molecules (out of 4 requested) 62: Replaced 8 residues (24 atoms) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 62: 62: Output configuration contains 632 atoms in 212 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (7 ms) 62: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Using random seed 1997 62: Read 4 positions from file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 62: 62: Try 1 success (now 2 atoms)! 62: Try 2 success (now 4 atoms)! 62: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 62: Try 13 success (now 6 atoms)! 62: 62: Added 3 molecules (out of 4 requested) 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 62: 62: Output configuration contains 6 atoms in 3 residues 62: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (3 ms) 62: [----------] 6 tests from InsertMoleculesTest (29 ms total) 62: 62: [----------] 3 tests from MassRepartitioning 62: [ RUN ] MassRepartitioning.ValidCaseWorks 62: The smallest mass in the system is 2, setting the minimum mass to 6 62: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 62: [ RUN ] MassRepartitioning.UnboundGivesWarning 62: 62: WARNING 1 [file unknown]: 62: The are 1 atoms that have a mass below the mass repartitioning limit but 62: are not bound. These masses cannot be repartitioned. 62: 62: The smallest mass in the system is 2, setting the minimum mass to 6 62: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 62: [ RUN ] MassRepartitioning.LightPartnerGivesError 62: 62: ERROR 1 [file unknown]: 62: Light atoms are bound to at least one atom that has a too low mass for 62: repartitioning 62: 62: The smallest mass in the system is 2, setting the minimum mass to 6 62: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 62: [----------] 3 tests from MassRepartitioning (0 ms total) 62: 62: [----------] 36 tests from GetIrTest 62: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 62: Ignoring obsolete mdp entry 'title' 62: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (6 ms) 62: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 62: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (11 ms) 62: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsKeyWithoutValue (6 ms) 62: [ RUN ] GetIrTest.RejectsValueWithoutKey 62: [ OK ] GetIrTest.RejectsValueWithoutKey (10 ms) 62: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 62: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (10 ms) 62: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (6 ms) 62: [ RUN ] GetIrTest.AcceptsEmptyLines 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsEmptyLines (6 ms) 62: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 62: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.MtsCheckNstcalcenergy (5 ms) 62: [ RUN ] GetIrTest.MtsCheckNstenergy 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 62: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (5) 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.MtsCheckNstenergy (5 ms) 62: [ RUN ] GetIrTest.MtsCheckNstpcouple 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 62: Pressure coupling incorrect number of values (I need exactly 1) 62: 62: 62: ERROR 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 62: Pressure coupling incorrect number of values (I need exactly 1) 62: 62: 62: ERROR 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 62: With multiple time stepping, nstpcouple should be a multiple of 62: mts-factor 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: ERROR 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 62: The Berendsen barostat does not generate any strictly correct ensemble, 62: and should not be used for new production simulations (in our opinion). 62: We recommend using the C-rescale barostat instead. 62: 62: 62: ERROR 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 62: compressibility must be > 0 when using pressure coupling Berendsen 62: 62: 62: [ OK ] GetIrTest.MtsCheckNstpcouple (5 ms) 62: [ RUN ] GetIrTest.MtsCheckNstdhdl 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 62: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstdhdl (5) 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: ERROR 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 62: Lambda state must be set, either with init-lambda-state or with 62: init-lambda 62: 62: [ OK ] GetIrTest.MtsCheckNstdhdl (5 ms) 62: [ RUN ] GetIrTest.MtsCheckSDNotSupported 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 62: Multiple time stepping is only supported with integrator md 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.MtsCheckSDNotSupported (5 ms) 62: [ RUN ] GetIrTest.AcceptsElectricField 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsElectricField (6 ms) 62: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (6 ms) 62: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (6 ms) 62: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 62: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (4 ms) 62: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsImplicitSolventNo (6 ms) 62: [ RUN ] GetIrTest.RejectsImplicitSolventYes 62: [ OK ] GetIrTest.RejectsImplicitSolventYes (13 ms) 62: [ RUN ] GetIrTest.AcceptsMimic 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsMimic (6 ms) 62: [ RUN ] GetIrTest.AcceptsTransformationCoord 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 62: pull-coord2 has a non-zero force constant and is also referenced in 62: pull-coord1-expression. Make sure that this is intended. In most use 62: cases, the pull coordinates referenced by a transformation coordinate 62: should have their force constant set to zero. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsTransformationCoord (6 ms) 62: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 62: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (5 ms) 62: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 62: pull-coord2 can not use pull-coord1 in the transformation since this is a 62: constraint 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (6 ms) 62: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 62: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 62: 'transformation' 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (5 ms) 62: [ RUN ] GetIrTest.MissingTransformationCoordExpression 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 62: pull-coord1-expression not set for pull coordinate of geometry 62: 'transformation' 62: 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.MissingTransformationCoordExpression (5 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 62: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 62: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 62: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 62: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 62: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 62: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 62: in total 100001 steps. This is not compatible with using soft-core 62: potentials. 62: 62: 62: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (5 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 62: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 62: won't change anymore after step 100000 until the end of the simulation 62: after 100001 steps. 62: 62: 62: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (5 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 62: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 62: won't change anymore after step 100000 until the end of the simulation 62: after 100001 steps. 62: 62: 62: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (5 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 62: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 62: components won't change anymore after step 100000 until the end of the 62: simulation after 100001 steps. 62: 62: 62: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (5 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 62: 62: ERROR 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 62: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 62: components won't change anymore after step 100000 until the end of the 62: simulation after 100001 steps. 62: 62: 62: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (5 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 62: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (4 ms) 62: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 62: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (4 ms) 62: [ RUN ] GetIrTest.AcceptsFmmOptions 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsFmmOptions_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ OK ] GetIrTest.AcceptsFmmOptions (6 ms) 62: [----------] 36 tests from GetIrTest (229 ms total) 62: 62: [----------] 6 tests from SolvateTest 62: [ RUN ] SolvateTest.cs_box_Works 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 1x1x1 boxes 62: Solvent box contains 270 atoms in 90 residues 62: Removed 129 solvent atoms due to solvent-solvent overlap 62: Sorting configuration 62: Found 1 molecule type: 62: SOL ( 3 atoms): 47 residues 62: Generated solvent containing 141 atoms in 47 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 62: 62: Output configuration contains 141 atoms in 47 residues 62: Volume : 1.331 (nm^3) 62: Density : 1056.36 (g/l) 62: Number of solvent molecules: 47 62: 62: [ OK ] SolvateTest.cs_box_Works (6 ms) 62: [ RUN ] SolvateTest.cs_cp_Works 62: Reading solute configuration 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 2x2x2 boxes 62: Solvent box contains 3660 atoms in 1220 residues 62: Removed 987 solvent atoms due to solvent-solvent overlap 62: Removed 15 solvent atoms due to solute-solvent overlap 62: Sorting configuration 62: Found 1 molecule type: 62: SOL ( 3 atoms): 886 residues 62: Generated solvent containing 2658 atoms in 886 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 62: 62: Output configuration contains 2664 atoms in 888 residues 62: Volume : 27.2709 (nm^3) 62: Density : 974.777 (g/l) 62: Number of solvent molecules: 886 62: 62: [ OK ] SolvateTest.cs_cp_Works (31 ms) 62: [ RUN ] SolvateTest.cs_cp_p_Works 62: Reading solute configuration 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 2x2x2 boxes 62: Solvent box contains 3660 atoms in 1220 residues 62: Removed 987 solvent atoms due to solvent-solvent overlap 62: Removed 15 solvent atoms due to solute-solvent overlap 62: Sorting configuration 62: Found 1 molecule type: 62: SOL ( 3 atoms): 886 residues 62: Generated solvent containing 2658 atoms in 886 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 62: 62: Output configuration contains 2664 atoms in 888 residues 62: Volume : 27.2709 (nm^3) 62: Density : 974.777 (g/l) 62: Number of solvent molecules: 886 62: 62: Processing topology 62: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 62: [ OK ] SolvateTest.cs_cp_p_Works (33 ms) 62: [ RUN ] SolvateTest.shell_Works 62: Reading solute configuration 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 2x2x2 boxes 62: Solvent box contains 3660 atoms in 1220 residues 62: Removed 987 solvent atoms due to solvent-solvent overlap 62: Removed 1902 solvent atoms more than 1.000000 nm from solute. 62: Removed 15 solvent atoms due to solute-solvent overlap 62: Sorting configuration 62: Found 1 molecule type: 62: SOL ( 3 atoms): 252 residues 62: Generated solvent containing 756 atoms in 252 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 62: 62: Output configuration contains 762 atoms in 254 residues 62: Volume : 27.2709 (nm^3) 62: Density : 279.3 (g/l) 62: Number of solvent molecules: 252 62: 62: [ OK ] SolvateTest.shell_Works (20 ms) 62: [ RUN ] SolvateTest.update_Topology_Works 62: Reading solute configuration 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 3x3x3 boxes 62: Solvent box contains 14952 atoms in 4984 residues 62: Removed 2787 solvent atoms due to solvent-solvent overlap 62: Removed 30 solvent atoms due to solute-solvent overlap 62: Sorting configuration 62: Found 2 different molecule types: 62: HOH ( 3 atoms): 1876 residues 62: SOL ( 3 atoms): 2169 residues 62: Generated solvent containing 0 atoms in 0 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 62: 62: Output configuration contains 12141 atoms in 4047 residues 62: Volume : 125 (nm^3) 62: Density : 968.963 (g/l) 62: Number of solvent molecules: 4045 62: 62: Processing topology 62: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 62: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 62: [ OK ] SolvateTest.update_Topology_Works (169 ms) 62: [ RUN ] SolvateTest.cs_pdb_big_box_Works 62: Reading solvent configuration 62: 62: Initialising inter-atomic distances... 62: 62: WARNING: Masses and atomic (Van der Waals) radii will be guessed 62: based on residue and atom names, since they could not be 62: definitively assigned from the information in your input 62: files. These guessed numbers might deviate from the mass 62: and radius of the atom type. Please check the output 62: files if necessary. Note, that this functionality may 62: be removed in a future GROMACS version. Please, consider 62: using another file format for your input. 62: 62: The atomic radii are set according to: 62: 62: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 62: A. Bondi 62: van der Waals Volumes and Radii 62: J. Phys. Chem. (1964) 62: https://doi.org/10.1021/j100785a001 62: -------- -------- --- Thank You --- -------- -------- 62: 62: Generating solvent configuration 62: Will generate new solvent configuration of 2x2x2 boxes 62: Solvent box contains 1218 atoms in 406 residues 62: Removed 555 solvent atoms due to solvent-solvent overlap 62: Sorting configuration 62: Found 1 molecule type: 62: SOL ( 3 atoms): 221 residues 62: Generated solvent containing 663 atoms in 221 residues 62: Writing generated configuration to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 62: 62: Output configuration contains 663 atoms in 221 residues 62: Volume : 8 (nm^3) 62: Density : 826.409 (g/l) 62: Number of solvent molecules: 221 62: 62: [ OK ] SolvateTest.cs_pdb_big_box_Works (12 ms) 62: [----------] 6 tests from SolvateTest (275 ms total) 62: 62: [----------] 1 test from TopDirTests 62: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 62: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 62: [----------] 1 test from TopDirTests (0 ms total) 62: 62: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Bond (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Morse (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Cubic_Bonds (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Connect_Bonds (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Harmonic_Pot_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/FENE_Bonds (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Bonds_NC (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restraint_Pot_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/G96Angle (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Angles (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Lin__Angle (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Bond_Cross (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/BA_Cross (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/U_B (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quartic_Angles (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Angles (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Proper_Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ryckaert_Bell_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Restr__Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CBT_Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Fourier_Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Improper_Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Per__Imp__Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Tab__Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/CMAP_Dih_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_14 (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_14_q (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJC_Pairs_NB (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Polarization (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Water_Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Thole_Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Anharm__Pol_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Position_Rest_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Flat_b__P_R_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dis__Rest_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Orient__Rest_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Angle_Rest__Z (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constraint (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Constr__No_Co_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Settle (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_1 (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_2 (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_2fd (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_3 (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_3fd (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3fad (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_3out (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virt__site_4fd (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__site_4fdn (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N 62: [ OK ] InteractionFunctionKind/ConvertInteractionsTest.Works/Virtual_site_N (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl (0 ms) 62: [ RUN ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 62: ./src/gromacs/gmxpreprocess/tests/convparm.cpp:133: Skipped 62: Skipping interaction type that does not represent a interaction with parameters converted in grompp 62: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl (0 ms) 62: [----------] 95 tests from InteractionFunctionKind/ConvertInteractionsTest (3 ms total) 62: 62: [----------] 16 tests from CorrectVelocity/MaxwellTest 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (3 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (5 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (2 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (2 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (2 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (2 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (2 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (2 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (1 ms) 62: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 62: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (2 ms) 62: [----------] 16 tests from CorrectVelocity/MaxwellTest (38 ms total) 62: 62: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_0_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -151781457 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -139200609 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/0 (10 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_1_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -587751443 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -85549714 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/1 (10 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_2_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -67256775 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -505446927 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/2 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_3_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -1979769092 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -5473921 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/3 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_4_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -8522307 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1738670170 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/4 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_5_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -545261826 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 1852829350 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/5 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_6_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to 1845329659 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -8409111 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/6 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_7_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to 933092791 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -941957637 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/7 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_8_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -138961922 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -77816291 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/8 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_9_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -153278511 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to 2075655999 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/9 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_10_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -672153697 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -273219713 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/10 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_11_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -168315907 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1210847762 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/11 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_12_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to 2127554031 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -58855425 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/12 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_13_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to 1593825215 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -9438253 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/13 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_14_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -914768002 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -1223436564 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/14 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_15_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -939787265 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -809518259 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/15 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_16_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -537014850 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 1 and kept 0 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -1123360773 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/16 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_17_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -1361324077 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -307300361 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/17 (9 ms) 62: [ RUN ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives.top, line 102]: 62: In moleculetype 'A' 6 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/DihedralAtomOrdering_GromppDirectiveTest_LEaPImproperDihedralAtomReordering_18_directives.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 62: Setting the LD random seed to -1111510369 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: To match AMBER LEaP ordering, reordered 0 and kept 1 Per. Imp. Dih. ordered as encountered (1 Per. Imp. Dih. types total) 62: 62: Setting gen_seed to -526442 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DihedralAtomOrdering/GromppDirectiveTest.LEaPImproperDihedralAtomReordering/18 (9 ms) 62: [----------] 19 tests from DihedralAtomOrdering/GromppDirectiveTest (181 ms total) 62: 62: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 62: Setting the LD random seed to -1075982738 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/0 (14 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 62: Setting the LD random seed to -2260995 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/1 (12 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_2_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -13701121 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -403284101 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/2 (9 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_3_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to 2031614332 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -286863489 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/3 (8 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_4_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to 134053887 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 1549761277 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/4 (8 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_5_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -774148609 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 1606941672 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/5 (8 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 62: Setting the LD random seed to 804121581 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/6 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 62: Setting the LD random seed to -445710337 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -67633957 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/7 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 62: Setting the LD random seed to -701014146 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/8 (12 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 62: Setting the LD random seed to -49291 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1623965817 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/9 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 62: Setting the LD random seed to 1874829304 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -25892961 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/10 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 62: Setting the LD random seed to -100737057 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -202424897 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/11 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 62: Setting the LD random seed to -638593830 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 1939831598 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/12 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 62: Setting the LD random seed to -269484097 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 871362527 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/13 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 62: Setting the LD random seed to 1526724326 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 2078799831 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/14 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 62: Setting the LD random seed to -140649729 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -318817569 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/15 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_16_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -92405859 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to 2147417550 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/16 (9 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_17_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -705175761 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -570968593 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/17 (8 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 62: Setting the LD random seed to 1340055755 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/18 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 62: Setting the LD random seed to -673710099 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -68732933 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/19 (14 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 62: Setting the LD random seed to 1570766323 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/20 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 62: Ignoring obsolete mdp entry 'title' 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file directives-cmap.top, line 121]: 62: In moleculetype 'A' 5 atoms are not bound by a potential or constraint to 62: any other atom in the same moleculetype. Although technically this might 62: not cause issues in a simulation, this often means that the user forgot 62: to add a bond/potential/constraint or put multiple molecules in the same 62: moleculetype definition by mistake. Run with -v to get information for 62: each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 12.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/CMAPDefinesAndErrors_GromppCmapDirectiveTest_AcceptValidAndErrorOnInvalidCMAP_21_directives-cmap.mdp]: 62: NVE simulation: will use the initial temperature of 300.000 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Setting the LD random seed to -44056693 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -810614786 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: Analysing residue names: 62: There are: 1 Other residues 62: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/21 (9 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 62: Setting the LD random seed to -537927681 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/22 (13 ms) 62: [ RUN ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 62: Setting the LD random seed to -28398121 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 0 bonded neighbours molecule type 'A' 62: 62: Setting gen_seed to -1076897794 62: 62: Velocities were taken from a Maxwell distribution at 300 K 62: [ OK ] CMAPDefinesAndErrors/GromppCmapDirectiveTest.AcceptValidAndErrorOnInvalidCMAP/23 (13 ms) 62: [----------] 24 tests from CMAPDefinesAndErrors/GromppCmapDirectiveTest (291 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 237 tests from 16 test suites ran. (3112 ms total) 62: [ PASSED ] 197 tests. 62: [ SKIPPED ] 40 tests, listed below: 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_2_Pol_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_3_Pol_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_1_4_Pol_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/GB_Polariz_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Nonpolar_Sol_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb_14 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ__SR_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Buck_ham__SR_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/B_ham 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Disper__corr_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coulomb__SR_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/RF_excl_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Coul__recip_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/LJ_recip_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/DPD 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/D_R_Viol___nm_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Ori__R__RMSD 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dih__Rest__Vi_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/COM_Pull_En_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Dens__fitting 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Quantum_En_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/NN_Potential 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Potential 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Kinetic_En_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Total_Energy 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Conserved_En_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Temperature 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Vir__Temp_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pres__DC 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/Pressure 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dH_dl_constr_ 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVremain_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dEkin_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVcoul_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVvdw_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVbonded_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVrestraint_dl 62: [ SKIPPED ] InteractionFunctionKind/ConvertInteractionsTest.Works/dVtemp_dl 62/103 Test #62: GmxPreprocessTests ........................ Passed 3.15 sec test 63 Start 63: Pdb2gmx1Test 63: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 63: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests 63: Test timeout computed to be: 1920 63: [==========] Running 30 tests from 1 test suite. 63: [----------] Global test environment set-up. 63: [----------] 30 tests from Oplsaa/Pdb2gmxTest 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 0 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (60 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 0 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (64 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 0 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (58 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 0 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (55 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 0 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (169 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Marked 124 virtual sites 63: Added 16 dummy masses 63: Added 26 new constraints 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 130 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (84 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Marked 132 virtual sites 63: Added 10 dummy masses 63: Added 19 new constraints 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 133 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (68 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Marked 123 virtual sites 63: Added 22 dummy masses 63: Added 35 new constraints 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 132 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Marked 111 virtual sites 63: Added 18 dummy masses 63: Added 31 new constraints 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 116 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (59 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Marked 447 virtual sites 63: Added 58 dummy masses 63: Added 101 new constraints 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 462 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip3p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (192 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 0 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (58 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 0 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (62 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 0 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (57 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 0 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (53 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 0 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (164 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Marked 124 virtual sites 63: Added 16 dummy masses 63: Added 26 new constraints 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 130 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (82 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Marked 132 virtual sites 63: Added 10 dummy masses 63: Added 19 new constraints 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 133 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (71 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Marked 123 virtual sites 63: Added 22 dummy masses 63: Added 35 new constraints 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 132 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Marked 111 virtual sites 63: Added 18 dummy masses 63: Added 31 new constraints 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 116 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (58 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Marked 447 virtual sites 63: Added 58 dummy masses 63: Added 101 new constraints 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 462 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip4p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (190 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 0 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (56 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 0 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (62 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 0 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (58 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 0 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (53 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 0 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (164 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 25 donors and 23 acceptors were found. 63: There are 41 hydrogen bonds 63: Will use HISE for residue 8 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS3 HIS8 63: SG9 NE251 63: HIS8 NE251 1.055 63: MET12 SD83 0.763 0.990 63: Marked 124 virtual sites 63: Added 16 dummy masses 63: Added 26 new constraints 63: Before cleaning: 653 pairs 63: Before cleaning: 663 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 63: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 128 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (128 atoms, 16 residues) 63: 63: Identified residue ALA2 as a starting terminus. 63: 63: Identified residue SER17 as a ending terminus. 63: Start terminus ALA-2: NH3+ 63: End terminus SER-17: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 252 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 254, now 254 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 663 dihedrals, 51 impropers, 457 angles 63: 650 pairs, 254 bonds and 130 virtual sites 63: 63: Total mass 1846.112 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (81 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 30 donors and 22 acceptors were found. 63: There are 36 hydrogen bonds 63: Will use HISE for residue 29 63: Will use HISE for residue 32 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS27 HIS29 63: SG90 NE2111 63: HIS29 NE2111 0.987 63: HIS32 NE2135 1.590 1.155 63: Marked 132 virtual sites 63: Added 10 dummy masses 63: Added 19 new constraints 63: Before cleaning: 748 pairs 63: Before cleaning: 778 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 63: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 149 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (149 atoms, 16 residues) 63: 63: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue THR18 as a starting terminus. 63: 63: Identified residue PHE33 as a ending terminus. 63: Start terminus THR-18: NH3+ 63: End terminus PHE-33: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 281 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 290, now 290 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 778 dihedrals, 72 impropers, 516 angles 63: 736 pairs, 290 bonds and 133 virtual sites 63: 63: Total mass 2088.357 a.m.u. 63: 63: Total charge 1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (68 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 22 acceptors were found. 63: There are 26 hydrogen bonds 63: Will use HISE for residue 45 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS45 63: NE295 63: MET46 SD102 1.078 63: Marked 123 virtual sites 63: Added 22 dummy masses 63: Added 35 new constraints 63: Before cleaning: 676 pairs 63: Before cleaning: 696 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 63: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 132 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (132 atoms, 16 residues) 63: 63: Identified residue ALA34 as a starting terminus. 63: 63: Identified residue ALA49 as a ending terminus. 63: Start terminus ALA-34: NH3+ 63: End terminus ALA-49: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 255 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 261, now 261 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 696 dihedrals, 56 impropers, 472 angles 63: 667 pairs, 261 bonds and 132 virtual sites 63: 63: Total mass 1861.128 a.m.u. 63: 63: Total charge -1.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (63 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 22 donors and 21 acceptors were found. 63: There are 30 hydrogen bonds 63: Will use HISE for residue 60 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: HIS60 63: NE285 63: CYS62 SG98 0.803 63: Marked 111 virtual sites 63: Added 18 dummy masses 63: Added 31 new constraints 63: Before cleaning: 603 pairs 63: Before cleaning: 618 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 63: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 63: 63: chain #res #atoms 63: 63: 1 ' ' 16 117 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 (117 atoms, 16 residues) 63: 63: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 63: 63: Identified residue LYS50 as a starting terminus. 63: 63: Identified residue PRO65 as a ending terminus. 63: Start terminus LYS-50: NH3+ 63: End terminus PRO-65: PRO-COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 16 residues with 228 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 232, now 232 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 618 dihedrals, 48 impropers, 419 angles 63: 597 pairs, 232 bonds and 116 virtual sites 63: 63: Total mass 1662.883 a.m.u. 63: 63: Total charge 0.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (57 ms) 63: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.r2b 63: All occupancies are one 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/atomtypes.atp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.rtp 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.hdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.n.tdb 63: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/oplsaa.ff/aminoacids.c.tdb 63: Analysing hydrogen-bonding network for automated assignment of histidine 63: protonation. 89 donors and 98 acceptors were found. 63: There are 129 hydrogen bonds 63: Will use HISE for residue 31 63: Will use HISE for residue 51 63: 9 out of 9 lines of specbond.dat converted successfully 63: Special Atom Distance matrix: 63: CYS25 HIS31 HIS51 63: SG14 NE264 NE2226 63: HIS31 NE264 1.921 63: HIS51 NE2226 1.498 2.650 63: CYS80 SG477 0.207 1.984 1.570 63: Linking CYS-25 SG-14 and CYS-80 SG-477... 63: Marked 447 virtual sites 63: Added 58 dummy masses 63: Added 101 new constraints 63: Before cleaning: 2499 pairs 63: Before cleaning: 2524 dihedrals 63: Using the Oplsaa force field in directory oplsaa.ff 63: 63: going to rename oplsaa.ff/aminoacids.r2b 63: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 63: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 63: 63: Analyzing pdb file 63: Splitting chemical chains based on TER records or chain id changing. 63: 63: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 63: 63: chain #res #atoms 63: 63: 1 'A' 58 488 63: 63: All occupancies are one 63: 63: Reading residue database... (Oplsaa) 63: 63: Preserving residues names by default 63: 63: Processing chain 1 'A' (488 atoms, 58 residues) 63: 63: Identified residue ASN24 as a starting terminus. 63: 63: Identified residue ARG81 as a ending terminus. 63: Start terminus ASN-24: NH3+ 63: End terminus ARG-81: COO- 63: 63: Checking for duplicate atoms.... 63: 63: Generating any missing hydrogen atoms and/or adding termini. 63: 63: Now there are 58 residues with 936 atoms 63: 63: Making bonds... 63: 63: Number of bonds was 951, now 951 63: 63: Generating angles, dihedrals and pairs... 63: 63: Making cmap torsions... 63: 63: There are 2524 dihedrals, 208 impropers, 1704 angles 63: 2469 pairs, 951 bonds and 462 virtual sites 63: 63: Total mass 6908.578 a.m.u. 63: 63: Total charge -6.000 e 63: 63: Writing topology 63: 63: Writing coordinate file... 63: 63: --------- PLEASE NOTE ------------ 63: 63: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 63: 63: The Oplsaa force field and the tip5p water model are used. 63: 63: --------- ETON ESAELP ------------ 63: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (191 ms) 63: [----------] 30 tests from Oplsaa/Pdb2gmxTest (2602 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 30 tests from 1 test suite ran. (2602 ms total) 63: [ PASSED ] 30 tests. 63/103 Test #63: Pdb2gmx1Test .............................. Passed 2.63 sec test 64 Start 64: Pdb2gmx2Test 64: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 64: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests 64: Test timeout computed to be: 1920 64: [==========] Running 40 tests from 2 test suites. 64: [----------] Global test environment set-up. 64: [----------] 20 tests from G43a1/Pdb2gmxTest 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 305 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 165 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 172, now 167 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 77 impropers, 241 angles 64: 267 pairs, 167 bonds and 0 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (73 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 429 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 202 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 216, now 211 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 134 impropers, 316 angles 64: 273 pairs, 211 bonds and 0 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (76 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 349 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 168 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 179, now 174 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 102 impropers, 260 angles 64: 242 pairs, 174 bonds and 0 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (71 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 299 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 150 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 159, now 154 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 80 impropers, 227 angles 64: 232 pairs, 154 bonds and 0 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (69 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1256 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 635 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 655, now 650 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 350 impropers, 955 angles 64: 972 pairs, 650 bonds and 0 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (137 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 37 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 305 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 165 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 172, now 167 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 77 impropers, 241 angles 64: 267 pairs, 167 bonds and 37 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (118 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 53 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 429 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 202 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 216, now 211 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 134 impropers, 316 angles 64: 273 pairs, 211 bonds and 51 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (89 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 36 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 349 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 168 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 179, now 174 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 102 impropers, 260 angles 64: 242 pairs, 174 bonds and 36 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (74 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 33 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 299 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 150 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 159, now 154 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 80 impropers, 227 angles 64: 232 pairs, 154 bonds and 31 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (70 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 146 virtual sites 64: Added 10 dummy masses 64: Added 29 new constraints 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1256 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 635 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 655, now 650 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 350 impropers, 955 angles 64: 972 pairs, 650 bonds and 137 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos43a1 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (144 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 305 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 165 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 172, now 167 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 77 impropers, 241 angles 64: 267 pairs, 167 bonds and 0 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (109 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 429 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 202 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 216, now 211 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 134 impropers, 316 angles 64: 273 pairs, 211 bonds and 0 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (75 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 349 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 168 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 179, now 174 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 102 impropers, 260 angles 64: 242 pairs, 174 bonds and 0 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (70 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 299 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 150 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 159, now 154 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 80 impropers, 227 angles 64: 232 pairs, 154 bonds and 0 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (68 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1256 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 635 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 655, now 650 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 350 impropers, 955 angles 64: 972 pairs, 650 bonds and 0 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (135 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 37 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 305 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 165 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 172, now 167 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 77 impropers, 241 angles 64: 267 pairs, 167 bonds and 37 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (123 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 53 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 429 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 202 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 216, now 211 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 134 impropers, 316 angles 64: 273 pairs, 211 bonds and 51 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (80 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 36 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 349 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 168 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 179, now 174 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 102 impropers, 260 angles 64: 242 pairs, 174 bonds and 36 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (74 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 33 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 299 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 150 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 159, now 154 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 80 impropers, 227 angles 64: 232 pairs, 154 bonds and 31 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (70 ms) 64: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.rtp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos43a1.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 146 virtual sites 64: Added 10 dummy masses 64: Added 29 new constraints 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1256 dihedrals 64: Using the Gromos43a1 force field in directory gromos43a1.ff 64: 64: going to rename gromos43a1.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos43a1) 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 635 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 655, now 650 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 350 impropers, 955 angles 64: 972 pairs, 650 bonds and 137 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos43a1 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (145 ms) 64: [----------] 20 tests from G43a1/Pdb2gmxTest (1880 ms total) 64: 64: [----------] 20 tests from G53a6/Pdb2gmxTest 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 312 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 167 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 174, now 169 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 79 impropers, 245 angles 64: 267 pairs, 169 bonds and 0 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (116 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 443 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 206 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 220, now 215 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 138 impropers, 324 angles 64: 273 pairs, 215 bonds and 0 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (86 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 356 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 170 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 181, now 176 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 104 impropers, 264 angles 64: 242 pairs, 176 bonds and 0 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (79 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 306 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 152 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 161, now 156 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 82 impropers, 231 angles 64: 232 pairs, 156 bonds and 0 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (76 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1270 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 639 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 659, now 654 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 354 impropers, 963 angles 64: 972 pairs, 654 bonds and 0 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (143 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 39 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 312 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 167 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 174, now 169 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 79 impropers, 245 angles 64: 267 pairs, 169 bonds and 39 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (81 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 57 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 443 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 206 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 220, now 215 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 138 impropers, 324 angles 64: 273 pairs, 215 bonds and 55 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (89 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 38 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 356 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 170 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 181, now 176 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 104 impropers, 264 angles 64: 242 pairs, 176 bonds and 38 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (81 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 35 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 306 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 152 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 161, now 156 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 82 impropers, 231 angles 64: 232 pairs, 156 bonds and 33 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (79 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 150 virtual sites 64: Added 10 dummy masses 64: Added 29 new constraints 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1270 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 639 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 659, now 654 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 354 impropers, 963 angles 64: 972 pairs, 654 bonds and 141 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos53a6 force field and the spc water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (218 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 312 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 167 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 174, now 169 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 79 impropers, 245 angles 64: 267 pairs, 169 bonds and 0 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (78 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 443 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 206 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 220, now 215 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 138 impropers, 324 angles 64: 273 pairs, 215 bonds and 0 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (85 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 356 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 170 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 181, now 176 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 104 impropers, 264 angles 64: 242 pairs, 176 bonds and 0 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (79 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 306 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 152 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 161, now 156 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 82 impropers, 231 angles 64: 232 pairs, 156 bonds and 0 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (76 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1270 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 639 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 659, now 654 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 354 impropers, 963 angles 64: 972 pairs, 654 bonds and 0 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (145 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 25 donors and 23 acceptors were found. 64: There are 41 hydrogen bonds 64: Will use HISE for residue 8 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS3 HIS8 64: SG9 NE251 64: HIS8 NE251 1.055 64: MET12 SD83 0.763 0.990 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 39 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 267 pairs 64: Before cleaning: 312 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 64: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 128 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (128 atoms, 16 residues) 64: 64: Identified residue ALA2 as a starting terminus. 64: 64: Identified residue SER17 as a ending terminus. 64: Start terminus ALA-2: NH3+ 64: End terminus SER-17: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 167 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 174, now 169 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 90 dihedrals, 79 impropers, 245 angles 64: 267 pairs, 169 bonds and 39 virtual sites 64: 64: Total mass 1846.116 a.m.u. 64: 64: Total charge 0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (123 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 30 donors and 22 acceptors were found. 64: There are 36 hydrogen bonds 64: Will use HISE for residue 29 64: Will use HISE for residue 32 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS27 HIS29 64: SG90 NE2111 64: HIS29 NE2111 0.987 64: HIS32 NE2135 1.590 1.155 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 57 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 273 pairs 64: Before cleaning: 443 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 64: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 149 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (149 atoms, 16 residues) 64: 64: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue THR18 as a starting terminus. 64: 64: Identified residue PHE33 as a ending terminus. 64: Start terminus THR-18: NH3+ 64: End terminus PHE-33: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 206 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 220, now 215 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 93 dihedrals, 138 impropers, 324 angles 64: 273 pairs, 215 bonds and 55 virtual sites 64: 64: Total mass 2088.361 a.m.u. 64: 64: Total charge 1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (87 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 22 acceptors were found. 64: There are 26 hydrogen bonds 64: Will use HISE for residue 45 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS45 64: NE295 64: MET46 SD102 1.078 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 38 virtual sites 64: Added 4 dummy masses 64: Added 8 new constraints 64: 64: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 242 pairs 64: Before cleaning: 356 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 64: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 132 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (132 atoms, 16 residues) 64: 64: Identified residue ALA34 as a starting terminus. 64: 64: Identified residue ALA49 as a ending terminus. 64: Start terminus ALA-34: NH3+ 64: End terminus ALA-49: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 170 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 181, now 176 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 81 dihedrals, 104 impropers, 264 angles 64: 242 pairs, 176 bonds and 38 virtual sites 64: 64: Total mass 1861.132 a.m.u. 64: 64: Total charge -1.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (82 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 22 donors and 21 acceptors were found. 64: There are 30 hydrogen bonds 64: Will use HISE for residue 60 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: HIS60 64: NE285 64: CYS62 SG98 0.803 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 35 virtual sites 64: Added 4 dummy masses 64: Added 10 new constraints 64: 64: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 232 pairs 64: Before cleaning: 306 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 64: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 64: 64: chain #res #atoms 64: 64: 1 ' ' 16 117 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 (117 atoms, 16 residues) 64: 64: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 64: 64: Identified residue LYS50 as a starting terminus. 64: 64: Identified residue PRO65 as a ending terminus. 64: Start terminus LYS-50: NH3+ 64: End terminus PRO-65: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 16 residues with 152 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 161, now 156 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 78 dihedrals, 82 impropers, 231 angles 64: 232 pairs, 156 bonds and 33 virtual sites 64: 64: Total mass 1662.887 a.m.u. 64: 64: Total charge -0.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (78 ms) 64: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.r2b 64: All occupancies are one 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/atomtypes.atp 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.rtp 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.hdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.n.tdb 64: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/gromos53a6.ff/aminoacids.c.tdb 64: Analysing hydrogen-bonding network for automated assignment of histidine 64: protonation. 89 donors and 98 acceptors were found. 64: There are 129 hydrogen bonds 64: Will use HISE for residue 31 64: Will use HISE for residue 51 64: 9 out of 9 lines of specbond.dat converted successfully 64: Special Atom Distance matrix: 64: CYS25 HIS31 HIS51 64: SG14 NE264 NE2226 64: HIS31 NE264 1.921 64: HIS51 NE2226 1.498 2.650 64: CYS80 SG477 0.207 1.984 1.570 64: Linking CYS-25 SG-14 and CYS-80 SG-477... 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: 64: WARNING: Duplicate line found in or between hackblock and rtp entries 64: 64: Marked 150 virtual sites 64: Added 10 dummy masses 64: Added 29 new constraints 64: 64: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom H used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: 64: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 64: to an entry in the topology database, but the atom O used in 64: an interaction of type angle in that entry is not found in the 64: input file. Perhaps your atom and/or residue naming needs to be 64: fixed. 64: 64: 64: Before cleaning: 972 pairs 64: Before cleaning: 1270 dihedrals 64: Using the Gromos53a6 force field in directory gromos53a6.ff 64: 64: going to rename gromos53a6.ff/aminoacids.r2b 64: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 64: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 64: 64: Analyzing pdb file 64: Splitting chemical chains based on TER records or chain id changing. 64: 64: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 64: 64: chain #res #atoms 64: 64: 1 'A' 58 488 64: 64: All occupancies are one 64: 64: Reading residue database... (Gromos53a6) 64: 64: Using default: not generating all possible dihedrals 64: 64: Using default: excluding 3 bonded neighbors 64: 64: Using default: generating 1,4 H--H interactions 64: 64: Using default: removing proper dihedrals found on the same bond as a proper dihedral 64: 64: Preserving residues names by default 64: 64: Processing chain 1 'A' (488 atoms, 58 residues) 64: 64: Identified residue ASN24 as a starting terminus. 64: 64: Identified residue ARG81 as a ending terminus. 64: Start terminus ASN-24: NH3+ 64: End terminus ARG-81: COO- 64: 64: Checking for duplicate atoms.... 64: 64: Generating any missing hydrogen atoms and/or adding termini. 64: 64: Now there are 58 residues with 639 atoms 64: 64: Making bonds... 64: 64: Number of bonds was 659, now 654 64: 64: Generating angles, dihedrals and pairs... 64: 64: Making cmap torsions... 64: 64: There are 321 dihedrals, 354 impropers, 963 angles 64: 972 pairs, 654 bonds and 141 virtual sites 64: 64: Total mass 6908.582 a.m.u. 64: 64: Total charge -6.000 e 64: 64: Writing topology 64: 64: Writing coordinate file... 64: 64: --------- PLEASE NOTE ------------ 64: 64: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 64: 64: The Gromos53a6 force field and the spce water model are used. 64: 64: --------- ETON ESAELP ------------ 64: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (156 ms) 64: [----------] 20 tests from G53a6/Pdb2gmxTest (2047 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 40 tests from 2 test suites ran. (3928 ms total) 64: [ PASSED ] 40 tests. 64/103 Test #64: Pdb2gmx2Test .............................. Passed 3.96 sec test 65 Start 65: Pdb2gmx3Test 65: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 65: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/gmxpreprocess/tests 65: Test timeout computed to be: 1920 65: [==========] Running 55 tests from 9 test suites. 65: [----------] Global test environment set-up. 65: [----------] 10 tests from Amber/Pdb2gmxTest 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Before cleaning: 653 pairs 65: Before cleaning: 691 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 255, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 691 dihedrals, 51 impropers, 457 angles 65: 650 pairs, 254 bonds and 0 virtual sites 65: 65: Total mass 1846.132 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (84 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Before cleaning: 748 pairs 65: Before cleaning: 788 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 291, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 788 dihedrals, 72 impropers, 516 angles 65: 736 pairs, 290 bonds and 0 virtual sites 65: 65: Total mass 2088.366 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (89 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Before cleaning: 676 pairs 65: Before cleaning: 727 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 262, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 727 dihedrals, 56 impropers, 472 angles 65: 667 pairs, 261 bonds and 0 virtual sites 65: 65: Total mass 1861.124 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (84 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Before cleaning: 603 pairs 65: Before cleaning: 634 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 233, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 634 dihedrals, 48 impropers, 419 angles 65: 597 pairs, 232 bonds and 0 virtual sites 65: 65: Total mass 1662.888 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (78 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Before cleaning: 2499 pairs 65: Before cleaning: 2631 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 952, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2631 dihedrals, 208 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 0 virtual sites 65: 65: Total mass 6908.576 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (212 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Marked 124 virtual sites 65: Added 16 dummy masses 65: Added 26 new constraints 65: Before cleaning: 653 pairs 65: Before cleaning: 691 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 255, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 691 dihedrals, 51 impropers, 457 angles 65: 650 pairs, 254 bonds and 130 virtual sites 65: 65: Total mass 1846.132 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (86 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Marked 132 virtual sites 65: Added 10 dummy masses 65: Added 19 new constraints 65: Before cleaning: 748 pairs 65: Before cleaning: 788 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 291, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 788 dihedrals, 72 impropers, 516 angles 65: 736 pairs, 290 bonds and 133 virtual sites 65: 65: Total mass 2088.366 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (96 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Marked 123 virtual sites 65: Added 22 dummy masses 65: Added 35 new constraints 65: Before cleaning: 676 pairs 65: Before cleaning: 727 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 262, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 727 dihedrals, 56 impropers, 472 angles 65: 667 pairs, 261 bonds and 132 virtual sites 65: 65: Total mass 1861.124 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (88 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Marked 111 virtual sites 65: Added 18 dummy masses 65: Added 31 new constraints 65: Before cleaning: 603 pairs 65: Before cleaning: 634 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 233, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 634 dihedrals, 48 impropers, 419 angles 65: 597 pairs, 232 bonds and 116 virtual sites 65: 65: Total mass 1662.888 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (82 ms) 65: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Marked 447 virtual sites 65: Added 58 dummy masses 65: Added 101 new constraints 65: Before cleaning: 2499 pairs 65: Before cleaning: 2631 dihedrals 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 952, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2631 dihedrals, 208 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 462 virtual sites 65: 65: Total mass 6908.576 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Amber99sb-ildn force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (233 ms) 65: [----------] 10 tests from Amber/Pdb2gmxTest (1136 ms total) 65: 65: [----------] 1 test from AmberTip4p/Pdb2gmxTest 65: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber99sb-ildn.ff/rna.arn 65: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 65: 65: going to rename amber99sb-ildn.ff/aminoacids.r2b 65: 65: going to rename amber99sb-ildn.ff/dna.r2b 65: 65: going to rename amber99sb-ildn.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 65: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 2 4 (only water) 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber99sb-ildn) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (4 atoms, 2 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 2 residues with 8 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 4, now 4 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 2 angles 65: 0 pairs, 4 bonds and 0 virtual sites 65: 65: Total mass 36.032 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 65: 65: The Amber99sb-ildn force field and the tip4p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (40 ms) 65: [----------] 1 test from AmberTip4p/Pdb2gmxTest (40 ms total) 65: 65: [----------] 10 tests from Amber14Sb/Pdb2gmxTest 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Before cleaning: 653 pairs 65: Before cleaning: 663 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 254, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 663 dihedrals, 51 impropers, 457 angles 65: 650 pairs, 254 bonds and 0 virtual sites 65: 65: Total mass 1846.132 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Amber14sb force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (64 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Before cleaning: 748 pairs 65: Before cleaning: 778 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 290, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 778 dihedrals, 76 impropers, 516 angles 65: 736 pairs, 290 bonds and 0 virtual sites 65: 65: Total mass 2088.366 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Amber14sb force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (70 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Before cleaning: 676 pairs 65: Before cleaning: 696 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 261, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 696 dihedrals, 58 impropers, 472 angles 65: 667 pairs, 261 bonds and 0 virtual sites 65: 65: Total mass 1861.124 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Amber14sb force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Before cleaning: 603 pairs 65: Before cleaning: 618 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 232, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 618 dihedrals, 48 impropers, 419 angles 65: 597 pairs, 232 bonds and 0 virtual sites 65: 65: Total mass 1662.888 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Amber14sb force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (60 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Before cleaning: 2499 pairs 65: Before cleaning: 2524 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 951, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2524 dihedrals, 210 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 0 virtual sites 65: 65: Total mass 6908.576 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Amber14sb force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (176 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Before cleaning: 653 pairs 65: Before cleaning: 663 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 254, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 663 dihedrals, 51 impropers, 457 angles 65: 650 pairs, 254 bonds and 0 virtual sites 65: 65: Total mass 1846.132 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Amber14sb force field and the opc3 water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (77 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Before cleaning: 748 pairs 65: Before cleaning: 778 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 290, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 778 dihedrals, 76 impropers, 516 angles 65: 736 pairs, 290 bonds and 0 virtual sites 65: 65: Total mass 2088.366 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Amber14sb force field and the opc3 water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (70 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Before cleaning: 676 pairs 65: Before cleaning: 696 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 261, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 696 dihedrals, 58 impropers, 472 angles 65: 667 pairs, 261 bonds and 0 virtual sites 65: 65: Total mass 1861.124 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Amber14sb force field and the opc3 water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Before cleaning: 603 pairs 65: Before cleaning: 618 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 232, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 618 dihedrals, 48 impropers, 419 angles 65: 597 pairs, 232 bonds and 0 virtual sites 65: 65: Total mass 1662.888 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Amber14sb force field and the opc3 water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (62 ms) 65: [ RUN ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber14sb.ff/aminoacids.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Before cleaning: 2499 pairs 65: Before cleaning: 2524 dihedrals 65: Using the Amber14sb force field in directory amber14sb.ff 65: 65: going to rename amber14sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber14sb) 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 951, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2524 dihedrals, 210 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 0 virtual sites 65: 65: Total mass 6908.576 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Amber14sb force field and the opc3 water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber14Sb/Pdb2gmxTest.Runs/ff_amber14sb_opc3_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (178 ms) 65: [----------] 10 tests from Amber14Sb/Pdb2gmxTest (891 ms total) 65: 65: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest 65: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Using the Amber19sb force field in directory amber19sb.ff 65: 65: going to rename amber19sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 65: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 2 4 (only water) 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber19sb) 65: 65: Processing chain 1 (4 atoms, 2 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 2 residues with 8 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 4, now 4 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 2 angles 65: 0 pairs, 4 bonds and 0 virtual sites 65: 65: Total mass 36.032 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 65: 65: The Amber19sb force field and the opc water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_opc_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (36 ms) 65: [ RUN ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber19sb.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Using the Amber19sb force field in directory amber19sb.ff 65: 65: going to rename amber19sb.ff/aminoacids.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 65: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 2 4 (only water) 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber19sb) 65: 65: Processing chain 1 (4 atoms, 2 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 2 residues with 8 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 4, now 4 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 2 angles 65: 0 pairs, 4 bonds and 0 virtual sites 65: 65: Total mass 36.032 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 65: 65: The Amber19sb force field and the tip4pew water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Amber19SbHo4/Pdb2gmxTest.Runs/ff_amber19sb_tip4pew_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (27 ms) 65: [----------] 2 tests from Amber19SbHo4/Pdb2gmxTest (64 ms total) 65: 65: [----------] 12 tests from Charmm/Pdb2gmxTest 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 653 pairs 65: Before cleaning: 663 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 254, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 663 dihedrals, 48 impropers, 457 angles 65: 650 pairs, 254 bonds and 0 virtual sites 65: 65: Total mass 1846.115 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (75 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 748 pairs 65: Before cleaning: 778 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 290, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 778 dihedrals, 49 impropers, 516 angles 65: 736 pairs, 290 bonds and 0 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (82 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 676 pairs 65: Before cleaning: 696 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 261, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 696 dihedrals, 39 impropers, 472 angles 65: 667 pairs, 261 bonds and 0 virtual sites 65: 65: Total mass 1861.130 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (80 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 603 pairs 65: Before cleaning: 618 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 232, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 618 dihedrals, 38 impropers, 419 angles 65: 597 pairs, 232 bonds and 0 virtual sites 65: 65: Total mass 1662.885 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (75 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 2499 pairs 65: Before cleaning: 2524 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 951, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 56 cmap torsion pairs 65: 65: There are 2524 dihedrals, 149 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 0 virtual sites 65: 65: Total mass 6908.566 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (183 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 39 pairs 65: Before cleaning: 39 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/monomer.pdb... 65: Read 'GLU', 9 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 65: 65: chain #res #atoms 65: 65: 1 'X' 1 9 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'X' (9 atoms, 1 residues) 65: 65: Identified residue GLU1 as a starting terminus. 65: 65: Identified residue GLU1 as a ending terminus. 65: Start terminus GLU-1: NH3+ 65: End terminus GLU-1: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 1 residues with 18 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 17, now 17 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 39 dihedrals, 2 impropers, 30 angles 65: 39 pairs, 17 bonds and 0 virtual sites 65: 65: Total mass 146.123 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/monomer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (41 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 124 virtual sites 65: Added 16 dummy masses 65: Added 26 new constraints 65: Before cleaning: 653 pairs 65: Before cleaning: 663 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 128 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (128 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 252 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 254, now 254 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 663 dihedrals, 48 impropers, 457 angles 65: 650 pairs, 254 bonds and 130 virtual sites 65: 65: Total mass 1846.115 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/A.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (81 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 30 donors and 22 acceptors were found. 65: There are 36 hydrogen bonds 65: Will use HISE for residue 29 65: Will use HISE for residue 32 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS27 HIS29 65: SG90 NE2111 65: HIS29 NE2111 0.987 65: HIS32 NE2135 1.590 1.155 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 132 virtual sites 65: Added 10 dummy masses 65: Added 19 new constraints 65: Before cleaning: 748 pairs 65: Before cleaning: 778 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb... 65: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 149 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (149 atoms, 16 residues) 65: 65: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue PHE33 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus PHE-33: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 281 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 290, now 290 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 778 dihedrals, 49 impropers, 516 angles 65: 736 pairs, 290 bonds and 133 virtual sites 65: 65: Total mass 2088.361 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/B.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (86 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 22 acceptors were found. 65: There are 26 hydrogen bonds 65: Will use HISE for residue 45 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS45 65: NE295 65: MET46 SD102 1.078 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 123 virtual sites 65: Added 22 dummy masses 65: Added 35 new constraints 65: Before cleaning: 676 pairs 65: Before cleaning: 696 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb... 65: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (132 atoms, 16 residues) 65: 65: Identified residue ALA34 as a starting terminus. 65: 65: Identified residue ALA49 as a ending terminus. 65: Start terminus ALA-34: NH3+ 65: End terminus ALA-49: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 261, now 261 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 696 dihedrals, 39 impropers, 472 angles 65: 667 pairs, 261 bonds and 132 virtual sites 65: 65: Total mass 1861.130 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/C.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (83 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 22 donors and 21 acceptors were found. 65: There are 30 hydrogen bonds 65: Will use HISE for residue 60 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS60 65: NE285 65: CYS62 SG98 0.803 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 111 virtual sites 65: Added 18 dummy masses 65: Added 31 new constraints 65: Before cleaning: 603 pairs 65: Before cleaning: 618 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb... 65: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 65: 65: chain #res #atoms 65: 65: 1 ' ' 16 117 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 (117 atoms, 16 residues) 65: 65: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 65: 65: Identified residue LYS50 as a starting terminus. 65: 65: Identified residue PRO65 as a ending terminus. 65: Start terminus LYS-50: NH3+ 65: End terminus PRO-65: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 228 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 232, now 232 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 14 cmap torsion pairs 65: 65: There are 618 dihedrals, 38 impropers, 419 angles 65: 597 pairs, 232 bonds and 116 virtual sites 65: 65: Total mass 1662.885 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/D.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (79 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 89 donors and 98 acceptors were found. 65: There are 129 hydrogen bonds 65: Will use HISE for residue 31 65: Will use HISE for residue 51 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS25 HIS31 HIS51 65: SG14 NE264 NE2226 65: HIS31 NE264 1.921 65: HIS51 NE2226 1.498 2.650 65: CYS80 SG477 0.207 1.984 1.570 65: Linking CYS-25 SG-14 and CYS-80 SG-477... 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 447 virtual sites 65: Added 58 dummy masses 65: Added 101 new constraints 65: Before cleaning: 2499 pairs 65: Before cleaning: 2524 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb... 65: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 58 488 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (488 atoms, 58 residues) 65: 65: Identified residue ASN24 as a starting terminus. 65: 65: Identified residue ARG81 as a ending terminus. 65: Start terminus ASN-24: NH3+ 65: End terminus ARG-81: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 58 residues with 936 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 951, now 951 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 56 cmap torsion pairs 65: 65: There are 2524 dihedrals, 149 impropers, 1704 angles 65: 2469 pairs, 951 bonds and 462 virtual sites 65: 65: Total mass 6908.566 a.m.u. 65: 65: Total charge -6.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/E.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (209 ms) 65: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Marked 8 virtual sites 65: Added 2 dummy masses 65: Added 3 new constraints 65: Before cleaning: 39 pairs 65: Before cleaning: 39 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/monomer.pdb... 65: Read 'GLU', 9 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 65: 65: chain #res #atoms 65: 65: 1 'X' 1 9 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'X' (9 atoms, 1 residues) 65: 65: Identified residue GLU1 as a starting terminus. 65: 65: Identified residue GLU1 as a ending terminus. 65: Start terminus GLU-1: NH3+ 65: End terminus GLU-1: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 1 residues with 18 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 17, now 17 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 39 dihedrals, 2 impropers, 30 angles 65: 39 pairs, 17 bonds and 9 virtual sites 65: 65: Total mass 146.123 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/monomer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (41 ms) 65: [----------] 12 tests from Charmm/Pdb2gmxTest (1125 ms total) 65: 65: [----------] 8 tests from ChainSep/Pdb2gmxTest 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 651 pairs 65: Before cleaning: 661 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on changing chain id only (ignoring TER records). 65: 65: Merged chains into joint molecule definitions at 2 places. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 16 127 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (127 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue GLU5 as a ending terminus. 65: 65: Identified residue PHE6 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus GLU-5: COO- 65: Start terminus PHE-6: NH3+ 65: End terminus MET-12: COO- 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 258 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 258, now 258 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 10 cmap torsion pairs 65: 65: There are 661 dihedrals, 46 impropers, 463 angles 65: 648 pairs, 258 bonds and 0 virtual sites 65: 65: Total mass 1882.146 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (75 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 123 pairs 65: Before cleaning: 123 dihedrals 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 10 donors and 7 acceptors were found. 65: There are 7 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: HIS8 65: NE223 65: MET12 SD55 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 317 pairs 65: Before cleaning: 322 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 211 pairs 65: Before cleaning: 216 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on changing chain id only (ignoring TER records). 65: 65: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 4 28 65: 65: 2 'B' 7 58 65: 65: 3 'C' 5 41 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (28 atoms, 4 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue GLU5 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus GLU-5: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 4 residues with 51 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 50, now 50 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2 cmap torsion pairs 65: 65: There are 123 dihedrals, 9 impropers, 88 angles 65: 123 pairs, 50 bonds and 0 virtual sites 65: 65: Total mass 434.421 a.m.u. 65: 65: Total charge -2.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (58 atoms, 7 residues) 65: 65: Identified residue PHE6 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: Start terminus PHE-6: NH3+ 65: End terminus MET-12: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 7 residues with 124 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 125, now 125 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 5 cmap torsion pairs 65: 65: There are 322 dihedrals, 19 impropers, 227 angles 65: 314 pairs, 125 bonds and 0 virtual sites 65: 65: Total mass 846.083 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Processing chain 3 'C' (41 atoms, 5 residues) 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 83 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 83, now 83 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 3 cmap torsion pairs 65: 65: There are 216 dihedrals, 18 impropers, 148 angles 65: 211 pairs, 83 bonds and 0 virtual sites 65: 65: Total mass 601.643 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 51 atoms 4 residues 65: 65: Including chain 2 in system: 124 atoms 7 residues 65: 65: Including chain 3 in system: 83 atoms 5 residues 65: 65: Now there are 258 atoms and 16 residues 65: 65: Total mass in system 1882.146 a.m.u. 65: 65: Total charge in system 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (65 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 651 pairs 65: Before cleaning: 661 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records only (ignoring chain id). 65: 65: Merged chains into joint molecule definitions at 2 places. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 16 127 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (127 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ILE9 as a ending terminus. 65: 65: Identified residue LYS10 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ILE-9: COO- 65: Start terminus LYS-10: NH3+ 65: End terminus MET-12: COO- 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 258 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 258, now 258 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 10 cmap torsion pairs 65: 65: There are 661 dihedrals, 46 impropers, 463 angles 65: 648 pairs, 258 bonds and 0 virtual sites 65: 65: Total mass 1882.146 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (77 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 10 donors and 12 acceptors were found. 65: There are 13 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 65: SG9 65: HIS8 NE251 1.055 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 288 pairs 65: Before cleaning: 293 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 152 pairs 65: Before cleaning: 152 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 211 pairs 65: Before cleaning: 216 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records only (ignoring chain id). 65: 65: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 8 61 65: 65: 2 'B' 3 25 65: 65: 3 'C' 5 41 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (61 atoms, 8 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ILE9 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ILE-9: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 8 residues with 114 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 115, now 115 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 6 cmap torsion pairs 65: 65: There are 293 dihedrals, 23 impropers, 203 angles 65: 285 pairs, 115 bonds and 0 virtual sites 65: 65: Total mass 888.952 a.m.u. 65: 65: Total charge -2.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (25 atoms, 3 residues) 65: 65: Identified residue LYS10 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: Start terminus LYS-10: NH3+ 65: End terminus MET-12: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 61 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 60, now 60 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 152 dihedrals, 5 impropers, 112 angles 65: 152 pairs, 60 bonds and 0 virtual sites 65: 65: Total mass 391.552 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Processing chain 3 'C' (41 atoms, 5 residues) 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 83 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 83, now 83 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 3 cmap torsion pairs 65: 65: There are 216 dihedrals, 18 impropers, 148 angles 65: 211 pairs, 83 bonds and 0 virtual sites 65: 65: Total mass 601.643 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 114 atoms 8 residues 65: 65: Including chain 2 in system: 61 atoms 3 residues 65: 65: Including chain 3 in system: 83 atoms 5 residues 65: 65: Now there are 258 atoms and 16 residues 65: 65: Total mass in system 1882.146 a.m.u. 65: 65: Total charge in system 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (70 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 650 pairs 65: Before cleaning: 660 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Merged chains into joint molecule definitions at 3 places. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 16 127 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (127 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue GLU5 as a ending terminus. 65: 65: Identified residue PHE6 as a starting terminus. 65: 65: Identified residue ILE9 as a ending terminus. 65: 65: Identified residue LYS10 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus GLU-5: COO- 65: Start terminus PHE-6: NH3+ 65: End terminus ILE-9: COO- 65: Start terminus LYS-10: NH3+ 65: End terminus MET-12: COO- 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 261 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 260, now 260 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 8 cmap torsion pairs 65: 65: There are 660 dihedrals, 45 impropers, 466 angles 65: 647 pairs, 260 bonds and 0 virtual sites 65: 65: Total mass 1900.162 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (81 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 65: 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 123 pairs 65: Before cleaning: 123 dihedrals 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 6 donors and 4 acceptors were found. 65: There are 3 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 164 pairs 65: Before cleaning: 169 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 152 pairs 65: Before cleaning: 152 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 211 pairs 65: Before cleaning: 216 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 65: 65: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 4 28 65: 65: 2 'B' 4 33 65: 65: 3 'B' 3 25 65: 65: 4 'C' 5 41 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (28 atoms, 4 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue GLU5 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus GLU-5: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 4 residues with 51 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 50, now 50 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2 cmap torsion pairs 65: 65: There are 123 dihedrals, 9 impropers, 88 angles 65: 123 pairs, 50 bonds and 0 virtual sites 65: 65: Total mass 434.421 a.m.u. 65: 65: Total charge -2.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (33 atoms, 4 residues) 65: 65: Identified residue PHE6 as a starting terminus. 65: 65: Identified residue ILE9 as a ending terminus. 65: Start terminus PHE-6: NH3+ 65: End terminus ILE-9: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 4 residues with 66 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 67, now 67 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2 cmap torsion pairs 65: 65: There are 169 dihedrals, 13 impropers, 118 angles 65: 161 pairs, 67 bonds and 0 virtual sites 65: 65: Total mass 472.547 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Processing chain 3 'B' (25 atoms, 3 residues) 65: 65: Identified residue LYS10 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: Start terminus LYS-10: NH3+ 65: End terminus MET-12: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 61 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 60, now 60 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 152 dihedrals, 5 impropers, 112 angles 65: 152 pairs, 60 bonds and 0 virtual sites 65: 65: Total mass 391.552 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Processing chain 4 'C' (41 atoms, 5 residues) 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 83 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 83, now 83 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 3 cmap torsion pairs 65: 65: There are 216 dihedrals, 18 impropers, 148 angles 65: 211 pairs, 83 bonds and 0 virtual sites 65: 65: Total mass 601.643 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 51 atoms 4 residues 65: 65: Including chain 2 in system: 66 atoms 4 residues 65: 65: Including chain 3 in system: 61 atoms 3 residues 65: 65: Including chain 4 in system: 83 atoms 5 residues 65: 65: Now there are 261 atoms and 16 residues 65: 65: Total mass in system 1900.162 a.m.u. 65: 65: Total charge in system 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (70 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 25 donors and 23 acceptors were found. 65: There are 41 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 652 pairs 65: Before cleaning: 662 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records and chain id changing. 65: 65: Merged chains into joint molecule definitions at 1 places. 65: 65: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 16 127 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (127 atoms, 16 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus MET-12: COO- 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 255 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 256, now 256 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 12 cmap torsion pairs 65: 65: There are 662 dihedrals, 47 impropers, 460 angles 65: 649 pairs, 256 bonds and 0 virtual sites 65: 65: Total mass 1864.131 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (78 ms) 65: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: Analysing hydrogen-bonding network for automated assignment of histidine 65: protonation. 14 donors and 15 acceptors were found. 65: There are 20 hydrogen bonds 65: Will use HISE for residue 8 65: 9 out of 9 lines of specbond.dat converted successfully 65: Special Atom Distance matrix: 65: CYS3 HIS8 65: SG9 NE251 65: HIS8 NE251 1.055 65: MET12 SD83 0.763 0.990 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 441 pairs 65: Before cleaning: 446 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 211 pairs 65: Before cleaning: 216 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 65: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records and chain id changing. 65: 65: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 11 86 65: 65: 2 'C' 5 41 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (86 atoms, 11 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue MET12 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus MET-12: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 11 residues with 172 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 173, now 173 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 9 cmap torsion pairs 65: 65: There are 446 dihedrals, 29 impropers, 312 angles 65: 438 pairs, 173 bonds and 0 virtual sites 65: 65: Total mass 1262.488 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'C' (41 atoms, 5 residues) 65: 65: Identified residue ASN13 as a starting terminus. 65: 65: Identified residue SER17 as a ending terminus. 65: Start terminus ASN-13: NH3+ 65: End terminus SER-17: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 83 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 83, now 83 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 3 cmap torsion pairs 65: 65: There are 216 dihedrals, 18 impropers, 148 angles 65: 211 pairs, 83 bonds and 0 virtual sites 65: 65: Total mass 601.643 a.m.u. 65: 65: Total charge 1.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 172 atoms 11 residues 65: 65: Including chain 2 in system: 83 atoms 5 residues 65: 65: Now there are 255 atoms and 16 residues 65: 65: Total mass in system 1864.131 a.m.u. 65: 65: Total charge in system 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (67 ms) 65: [----------] 8 tests from ChainSep/Pdb2gmxTest (589 ms total) 65: 65: [----------] 4 tests from ChainChanges/Pdb2gmxTest 65: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 83 pairs 65: Before cleaning: 83 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 145 pairs 65: Before cleaning: 150 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb... 65: Read 'Fragments of peptides and ions', 47 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on changing chain id only (ignoring TER records). 65: 65: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 3 19 65: 65: 2 'B' 3 28 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (19 atoms, 3 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ASP4 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ASP-4: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 36 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 35, now 35 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 83 dihedrals, 6 impropers, 61 angles 65: 83 pairs, 35 bonds and 0 virtual sites 65: 65: Total mass 306.314 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (28 atoms, 3 residues) 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue TRP20 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus TRP-20: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 57 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 58, now 58 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 150 dihedrals, 5 impropers, 103 angles 65: 142 pairs, 58 bonds and 0 virtual sites 65: 65: Total mass 404.468 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 36 atoms 3 residues 65: 65: Including chain 2 in system: 57 atoms 3 residues 65: 65: Now there are 93 atoms and 6 residues 65: 65: Total mass in system 710.782 a.m.u. 65: 65: Total charge in system -1.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (75 ms) 65: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 83 pairs 65: Before cleaning: 83 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 145 pairs 65: Before cleaning: 150 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb... 65: Read 'Fragments of peptides and ions', 47 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records only (ignoring chain id). 65: 65: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 3 19 65: 65: 2 'B' 3 28 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (19 atoms, 3 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ASP4 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ASP-4: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 36 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 35, now 35 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 83 dihedrals, 6 impropers, 61 angles 65: 83 pairs, 35 bonds and 0 virtual sites 65: 65: Total mass 306.314 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (28 atoms, 3 residues) 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue TRP20 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus TRP-20: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 57 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 58, now 58 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 150 dihedrals, 5 impropers, 103 angles 65: 142 pairs, 58 bonds and 0 virtual sites 65: 65: Total mass 404.468 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 36 atoms 3 residues 65: 65: Including chain 2 in system: 57 atoms 3 residues 65: 65: Now there are 93 atoms and 6 residues 65: 65: Total mass in system 710.782 a.m.u. 65: 65: Total charge in system -1.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (49 ms) 65: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 83 pairs 65: Before cleaning: 83 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 145 pairs 65: Before cleaning: 150 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb... 65: Read 'Fragments of peptides and ions', 47 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 3 19 65: 65: 2 'B' 3 28 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (19 atoms, 3 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ASP4 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ASP-4: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 36 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 35, now 35 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 83 dihedrals, 6 impropers, 61 angles 65: 83 pairs, 35 bonds and 0 virtual sites 65: 65: Total mass 306.314 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (28 atoms, 3 residues) 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue TRP20 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus TRP-20: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 57 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 58, now 58 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 150 dihedrals, 5 impropers, 103 angles 65: 142 pairs, 58 bonds and 0 virtual sites 65: 65: Total mass 404.468 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 36 atoms 3 residues 65: 65: Including chain 2 in system: 57 atoms 3 residues 65: 65: Now there are 93 atoms and 6 residues 65: 65: Total mass in system 710.782 a.m.u. 65: 65: Total charge in system -1.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (48 ms) 65: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 83 pairs 65: Before cleaning: 83 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 145 pairs 65: Before cleaning: 150 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb... 65: Read 'Fragments of peptides and ions', 47 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records and chain id changing. 65: 65: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 3 19 65: 65: 2 'B' 3 28 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (19 atoms, 3 residues) 65: 65: Identified residue ALA2 as a starting terminus. 65: 65: Identified residue ASP4 as a ending terminus. 65: Start terminus ALA-2: NH3+ 65: End terminus ASP-4: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 36 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 35, now 35 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 83 dihedrals, 6 impropers, 61 angles 65: 83 pairs, 35 bonds and 0 virtual sites 65: 65: Total mass 306.314 a.m.u. 65: 65: Total charge -1.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'B' (28 atoms, 3 residues) 65: 65: Identified residue THR18 as a starting terminus. 65: 65: Identified residue TRP20 as a ending terminus. 65: Start terminus THR-18: NH3+ 65: End terminus TRP-20: COO- 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 3 residues with 57 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 58, now 58 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 1 cmap torsion pairs 65: 65: There are 150 dihedrals, 5 impropers, 103 angles 65: 142 pairs, 58 bonds and 0 virtual sites 65: 65: Total mass 404.468 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 36 atoms 3 residues 65: 65: Including chain 2 in system: 57 atoms 3 residues 65: 65: Now there are 93 atoms and 6 residues 65: 65: Total mass in system 710.782 a.m.u. 65: 65: Total charge in system -1.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/fragments.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (48 ms) 65: [----------] 4 tests from ChainChanges/Pdb2gmxTest (222 ms total) 65: 65: [----------] 4 tests from Cyclic/Pdb2gmxTest 65: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: WARNING: all CONECT records are ignored 65: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 65: 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 6040 pairs 65: Before cleaning: 6605 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 6040 pairs 65: Before cleaning: 6605 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 65: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 65: 65: Moved all the water blocks to the end 65: 65: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 65: 65: chain #res #atoms 65: 65: 1 'P' 71 1527 65: 65: 2 'Q' 71 1527 65: 65: 3 'Q' 7 7 65: 65: 4 ' ' 10 10 (only water) 65: 65: 5 ' ' 16 16 (only water) 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'P' (1527 atoms, 71 residues) 65: 65: Identified residue G1 as a starting terminus. 65: 65: Identified residue U71 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 71 residues with 2297 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 2481, now 2481 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 6605 dihedrals, 183 impropers, 4434 angles 65: 5827 pairs, 2481 bonds and 0 virtual sites 65: 65: Total mass 22984.514 a.m.u. 65: 65: Total charge -71.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'Q' (1527 atoms, 71 residues) 65: 65: Identified residue G1 as a starting terminus. 65: 65: Identified residue U71 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 71 residues with 2297 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 2481, now 2481 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 6605 dihedrals, 183 impropers, 4434 angles 65: 5827 pairs, 2481 bonds and 0 virtual sites 65: 65: Total mass 22984.514 a.m.u. 65: 65: Total charge -71.000 e 65: 65: Writing topology 65: 65: Processing chain 3 'Q' (7 atoms, 7 residues) 65: 65: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 65: 65: Disabling further notes about ions. 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 7 residues with 7 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: No bonds 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 0 angles 65: 0 pairs, 0 bonds and 0 virtual sites 65: 65: Total mass 170.135 a.m.u. 65: 65: Total charge 14.000 e 65: 65: Writing topology 65: 65: Processing chain 4 (10 atoms, 10 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 10 residues with 30 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 30, now 30 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 30 angles 65: 0 pairs, 30 bonds and 0 virtual sites 65: 65: Total mass 180.154 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Processing chain 5 (16 atoms, 16 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain m9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: olecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 48 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 48, now 48 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 48 angles 65: 0 pairs, 48 bonds and 0 virtual sites 65: 65: Total mass 288.246 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Including chain 1 in system: 2297 atoms 71 residues 65: 65: Including chain 2 in system: 2297 atoms 71 residues 65: 65: Including chain 3 in system: 7 atoms 7 residues 65: 65: Including chain 4 in system: 30 atoms 10 residues 65: 65: Including chain 5 in system: 48 atoms 16 residues 65: 65: Now there are 4679 atoms and 175 residues 65: 65: Total mass in system 46607.563 a.m.u. 65: 65: Total charge in system -128.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (979 ms) 65: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 2325 pairs 65: Before cleaning: 2325 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 65: Read 'CARNOCYCLIN-A', 413 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 60 413 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (413 atoms, 60 residues) 65: 65: Identified residue LEU1 as a starting terminus. 65: 65: Identified residue LEU60 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 60 residues with 878 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 880, now 880 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 60 cmap torsion pairs 65: 65: There are 2325 dihedrals, 137 impropers, 1614 angles 65: 2319 pairs, 880 bonds and 0 virtual sites 65: 65: Total mass 5866.087 a.m.u. 65: 65: Total charge 4.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (206 ms) 65: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: WARNING: all CONECT records are ignored 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 12080 pairs 65: Before cleaning: 13210 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 65: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Moved all the water blocks to the end 65: 65: Merged chains into joint molecule definitions at 2 places. 65: 65: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 65: 65: chain #res #atoms 65: 65: 1 'P' 149 3061 65: 65: 2 ' ' 10 10 (only water) 65: 65: 3 ' ' 16 16 (only water) 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'P' (3061 atoms, 149 residues) 65: 65: Identified residue G1 as a starting terminus. 65: 65: Identified residue U71 as a ending terminus. 65: 65: Identified residue G1 as a starting terminus. 65: 65: Identified residue U71 as a ending terminus. 65: 65: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 65: 65: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 65: 65: Disabling further notes about ions. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 149 residues with 4601 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 4962, now 4962 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 13210 dihedrals, 366 impropers, 8868 angles 65: 11654 pairs, 4962 bonds and 0 virtual sites 65: 65: Total mass 46139.162 a.m.u. 65: 65: Total charge -128.000 e 65: 65: Writing topology 65: 65: Processing chain 2 (10 atoms, 10 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 10 residues with 30 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 30, now 30 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 30 angles 65: 0 pairs, 30 bonds and 0 virtual sites 65: 65: Total mass 180.154 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Processing chain 3 (16 atoms, 16 residues) 65: 65: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 16 residues with 48 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 48, now 48 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 0 dihedrals, 0 impropers, 48 angles 65: 0 pairs, 48 bonds and 0 virtual sites 65: 65: Total mass 288.246 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Including chain 1 in system: 4601 atoms 149 residues 65: 65: Including chain 2 in system: 30 atoms 10 residues 65: 65: Including chain 3 in system: 48 atoms 16 residues 65: 65: Now there are 4679 atoms and 175 residues 65: 65: Total mass in system 46607.563 a.m.u. 65: 65: Total charge in system -128.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (1090 ms) 65: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/lipids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.c.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/charmm27.ff/rna.arn 65: Before cleaning: 2325 pairs 65: Before cleaning: 2325 dihedrals 65: Using the Charmm27 force field in directory charmm27.ff 65: 65: going to rename charmm27.ff/aminoacids.r2b 65: 65: going to rename charmm27.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 65: Read 'CARNOCYCLIN-A', 413 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 65: 65: chain #res #atoms 65: 65: 1 'A' 60 413 65: 65: All occupancies are one 65: 65: Reading residue database... (Charmm27) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'A' (413 atoms, 60 residues) 65: 65: Identified residue LEU1 as a starting terminus. 65: 65: Identified residue LEU60 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 60 residues with 878 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 880, now 880 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 60 cmap torsion pairs 65: 65: There are 2325 dihedrals, 137 impropers, 1614 angles 65: 2319 pairs, 880 bonds and 0 virtual sites 65: 65: Total mass 5866.087 a.m.u. 65: 65: Total charge 4.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 65: 65: The Charmm27 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (211 ms) 65: [----------] 4 tests from Cyclic/Pdb2gmxTest (2488 ms total) 65: 65: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest 65: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 233 pairs 65: Before cleaning: 243 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 2325 pairs 65: Before cleaning: 2325 dihedrals 65: Using the Amber96 force field in directory amber96.ff 65: 65: going to rename amber96.ff/aminoacids.r2b 65: 65: going to rename amber96.ff/dna.r2b 65: 65: going to rename amber96.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 65: Read 'Two cyclic peptides, one small one big', 460 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 2 chains and 0 blocks of water and 65 residues with 460 atoms 65: 65: chain #res #atoms 65: 65: 1 'C' 5 47 65: 65: 2 'A' 60 413 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber96) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'C' (47 atoms, 5 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 86 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 89, now 89 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 243 dihedrals, 23 impropers, 159 angles 65: 230 pairs, 89 bonds and 0 virtual sites 65: 65: Total mass 653.702 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'A' (413 atoms, 60 residues) 65: 65: Identified residue LEU1 as a starting terminus. 65: 65: Identified residue LEU60 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 60 residues with 878 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 880, now 880 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2325 dihedrals, 141 impropers, 1614 angles 65: 2319 pairs, 880 bonds and 0 virtual sites 65: 65: Total mass 5866.100 a.m.u. 65: 65: Total charge 4.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 86 atoms 5 residues 65: 65: Including chain 2 in system: 878 atoms 60 residues 65: 65: Now there are 964 atoms and 65 residues 65: 65: Total mass in system 6519.802 a.m.u. 65: 65: Total charge in system 4.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 65: 65: The Amber96 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep1pdb_format_gro_match_file (217 ms) 65: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 188 pairs 65: Before cleaning: 198 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 233 pairs 65: Before cleaning: 243 dihedrals 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 233 pairs 65: Before cleaning: 243 dihedrals 65: Using the Amber96 force field in directory amber96.ff 65: 65: going to rename amber96.ff/aminoacids.r2b 65: 65: going to rename amber96.ff/dna.r2b 65: 65: going to rename amber96.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 65: Read 'One linear then two cyclic peptides', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: There are 3 chains and 0 blocks of water and 14 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 'C' 4 38 65: 65: 2 'E' 5 47 65: 65: 3 'F' 5 47 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber96) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'C' (38 atoms, 4 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue TRP4 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 4 residues with 72 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 75, now 74 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 198 dihedrals, 18 impropers, 132 angles 65: 185 pairs, 74 bonds and 0 virtual sites 65: 65: Total mass 543.584 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Processing chain 2 'E' (47 atoms, 5 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 86 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 89, now 89 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 243 dihedrals, 23 impropers, 159 angles 65: 230 pairs, 89 bonds and 0 virtual sites 65: 65: Total mass 653.702 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Processing chain 3 'F' (47 atoms, 5 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 5 residues with 86 atoms 65: Chain time... 65: 65: Making bonds... 65: 65: Number of bonds was 89, now 89 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 243 dihedrals, 23 impropers, 159 angles 65: 230 pairs, 89 bonds and 0 virtual sites 65: 65: Total mass 653.702 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Including chain 1 in system: 72 atoms 4 residues 65: 65: Including chain 2 in system: 86 atoms 5 residues 65: 65: Including chain 3 in system: 86 atoms 5 residues 65: 65: Now there are 244 atoms and 14 residues 65: 65: Total mass in system 1850.988 a.m.u. 65: 65: Total charge in system 0.000 e 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 65: 65: The Amber96 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_no_multcycpep2pdb_format_gro_match_file (87 ms) 65: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 2558 pairs 65: Before cleaning: 2568 dihedrals 65: Using the Amber96 force field in directory amber96.ff 65: 65: going to rename amber96.ff/aminoacids.r2b 65: 65: going to rename amber96.ff/dna.r2b 65: 65: going to rename amber96.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb... 65: Read 'Two cyclic peptides, one small one big', 460 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Merged chains into joint molecule definitions at 1 places. 65: 65: There are 1 chains and 0 blocks of water and 65 residues with 460 atoms 65: 65: chain #res #atoms 65: 65: 1 'C' 65 460 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber96) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'C' (460 atoms, 65 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Identified residue LEU1 as a starting terminus. 65: 65: Identified residue LEU60 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 65 residues with 964 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 969, now 969 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 2568 dihedrals, 164 impropers, 1773 angles 65: 2549 pairs, 969 bonds and 0 virtual sites 65: 65: Total mass 6519.802 a.m.u. 65: 65: Total charge 4.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-1.pdb. 65: 65: The Amber96 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep1pdb_format_gro_match_file (205 ms) 65: [ RUN ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.r2b 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.r2b 65: All occupancies are one 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/atomtypes.atp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.rtp 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.hdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.n.tdb 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.c.tdb 65: 9 out of 9 lines of specbond.dat converted successfully 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/aminoacids.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/dna.arn 65: Opening force field file /build/reproducible-path/gromacs-2026.2/share/top/amber96.ff/rna.arn 65: Before cleaning: 654 pairs 65: Before cleaning: 684 dihedrals 65: Using the Amber96 force field in directory amber96.ff 65: 65: going to rename amber96.ff/aminoacids.r2b 65: 65: going to rename amber96.ff/dna.r2b 65: 65: going to rename amber96.ff/rna.r2b 65: Reading /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb... 65: Read 'One linear then two cyclic peptides', 132 atoms 65: 65: Analyzing pdb file 65: Splitting chemical chains based on TER records or chain id changing. 65: 65: Merged chains into joint molecule definitions at 2 places. 65: 65: There are 1 chains and 0 blocks of water and 14 residues with 132 atoms 65: 65: chain #res #atoms 65: 65: 1 'C' 14 132 65: 65: All occupancies are one 65: 65: Reading residue database... (Amber96) 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Preserving residues names by default 65: 65: Processing chain 1 'C' (132 atoms, 14 residues) 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue TRP4 as a ending terminus. 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Identified residue ASN1 as a starting terminus. 65: 65: Identified residue GLN5 as a ending terminus. 65: 65: Checking for duplicate atoms.... 65: 65: Generating any missing hydrogen atoms and/or adding termini. 65: 65: Now there are 14 residues with 244 atoms 65: 65: Making bonds... 65: 65: Number of bonds was 253, now 252 65: 65: Generating angles, dihedrals and pairs... 65: 65: Making cmap torsions... 65: 65: There are 684 dihedrals, 64 impropers, 450 angles 65: 645 pairs, 252 bonds and 0 virtual sites 65: 65: Total mass 1850.988 a.m.u. 65: 65: Total charge 0.000 e 65: 65: Writing topology 65: 65: Writing coordinate file... 65: 65: --------- PLEASE NOTE ------------ 65: 65: You have successfully generated a topology from: /build/reproducible-path/gromacs-2026.2/src/gromacs/gmxpreprocess/tests/mult-cyc-pep-2.pdb. 65: 65: The Amber96 force field and the tip3p water model are used. 65: 65: --------- ETON ESAELP ------------ 65: [ OK ] MultipleCyclic/Pdb2gmxTest.Runs/ff_amber96_tip3p_vsite_none_id_or_ter_merge_all_multcycpep2pdb_format_gro_match_file (81 ms) 65: [----------] 4 tests from MultipleCyclic/Pdb2gmxTest (593 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 55 tests from 9 test suites ran. (7151 ms total) 65: [ PASSED ] 55 tests. 65/103 Test #65: Pdb2gmx3Test .............................. Passed 7.18 sec test 66 Start 66: CorrelationsTest 66: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 66: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/correlationfunctions/tests 66: Test timeout computed to be: 30 66: [==========] Running 21 tests from 3 test suites. 66: [----------] Global test environment set-up. 66: [----------] 10 tests from AutocorrTest 66: [ RUN ] AutocorrTest.EacNormal 66: [ OK ] AutocorrTest.EacNormal (5 ms) 66: [ RUN ] AutocorrTest.EacNoNormalize 66: [ OK ] AutocorrTest.EacNoNormalize (2 ms) 66: [ RUN ] AutocorrTest.EacCos 66: [ OK ] AutocorrTest.EacCos (4 ms) 66: [ RUN ] AutocorrTest.EacVector 66: [ OK ] AutocorrTest.EacVector (5 ms) 66: [ RUN ] AutocorrTest.EacRcross 66: [ OK ] AutocorrTest.EacRcross (1 ms) 66: [ RUN ] AutocorrTest.EacP0 66: [ OK ] AutocorrTest.EacP0 (7 ms) 66: [ RUN ] AutocorrTest.EacP1 66: [ OK ] AutocorrTest.EacP1 (7 ms) 66: [ RUN ] AutocorrTest.EacP2 66: [ OK ] AutocorrTest.EacP2 (16 ms) 66: [ RUN ] AutocorrTest.EacP3 66: [ OK ] AutocorrTest.EacP3 (5 ms) 66: [ RUN ] AutocorrTest.EacP4 66: [ OK ] AutocorrTest.EacP4 (8 ms) 66: [----------] 10 tests from AutocorrTest (66 ms total) 66: 66: [----------] 10 tests from ExpfitTest 66: [ RUN ] ExpfitTest.EffnEXP1 66: [ OK ] ExpfitTest.EffnEXP1 (1 ms) 66: [ RUN ] ExpfitTest.EffnEXP2 66: [ OK ] ExpfitTest.EffnEXP2 (1 ms) 66: [ RUN ] ExpfitTest.EffnEXPEXP 66: [ OK ] ExpfitTest.EffnEXPEXP (2 ms) 66: [ RUN ] ExpfitTest.EffnEXP5 66: [ OK ] ExpfitTest.EffnEXP5 (8 ms) 66: [ RUN ] ExpfitTest.EffnEXP7 66: [ OK ] ExpfitTest.EffnEXP7 (6 ms) 66: [ RUN ] ExpfitTest.EffnEXP9 66: [ OK ] ExpfitTest.EffnEXP9 (27 ms) 66: [ RUN ] ExpfitTest.EffnERF 66: [ OK ] ExpfitTest.EffnERF (4 ms) 66: [ RUN ] ExpfitTest.EffnERREST 66: [ OK ] ExpfitTest.EffnERREST (6 ms) 66: [ RUN ] ExpfitTest.EffnVAC 66: [ OK ] ExpfitTest.EffnVAC (16 ms) 66: [ RUN ] ExpfitTest.EffnPRES 66: [ OK ] ExpfitTest.EffnPRES (19 ms) 66: [----------] 10 tests from ExpfitTest (95 ms total) 66: 66: [----------] 1 test from ManyAutocorrelationTest 66: [ RUN ] ManyAutocorrelationTest.Empty 66: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 66: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 21 tests from 3 test suites ran. (174 ms total) 66: [ PASSED ] 21 tests. 66/103 Test #66: CorrelationsTest .......................... Passed 0.20 sec test 67 Start 67: AnalysisDataUnitTests 67: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/analysisdata/tests 67: Test timeout computed to be: 30 67: [==========] Running 69 tests from 14 test suites. 67: [----------] Global test environment set-up. 67: [----------] 3 tests from AnalysisDataInitializationTest 67: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 67: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 67: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 67: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 67: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 67: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 67: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 67: 67: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = gmx::test::(anonymous namespace)::SimpleInputData 67: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 67: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 67: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 67: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 67: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 67: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 67: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 67: [----------] 8 tests from AnalysisDataCommonTest/0 (3 ms total) 67: 67: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = gmx::test::(anonymous namespace)::DataSetsInputData 67: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 67: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 67: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 67: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 67: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 67: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 67: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 67: [----------] 8 tests from AnalysisDataCommonTest/1 (4 ms total) 67: 67: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = gmx::test::(anonymous namespace)::MultipointInputData 67: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 67: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 67: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 67: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 67: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 67: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 67: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 67: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 67: [----------] 8 tests from AnalysisDataCommonTest/2 (5 ms total) 67: 67: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = gmx::test::(anonymous namespace)::MultipointDataSetsInputData 67: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 67: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 67: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 67: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 67: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 67: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 67: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 67: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 67: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 67: [----------] 8 tests from AnalysisDataCommonTest/3 (5 ms total) 67: 67: [----------] 4 tests from AnalysisArrayDataTest 67: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 67: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 67: [ RUN ] AnalysisArrayDataTest.StorageWorks 67: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 67: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 67: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 67: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 67: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 67: [----------] 4 tests from AnalysisArrayDataTest (1 ms total) 67: 67: [----------] 6 tests from AverageModuleTest 67: [ RUN ] AverageModuleTest.BasicTest 67: [ OK ] AverageModuleTest.BasicTest (44 ms) 67: [ RUN ] AverageModuleTest.HandlesMultipointData 67: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 67: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 67: [ OK ] AverageModuleTest.HandlesMultipleDataSets (5 ms) 67: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 67: [ OK ] AverageModuleTest.HandlesDataSetAveraging (1 ms) 67: [ RUN ] AverageModuleTest.CanCustomizeXAxis 67: [ OK ] AverageModuleTest.CanCustomizeXAxis (1 ms) 67: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 67: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (1 ms) 67: [----------] 6 tests from AverageModuleTest (54 ms total) 67: 67: [----------] 2 tests from FrameAverageModuleTest 67: [ RUN ] FrameAverageModuleTest.BasicTest 67: [ OK ] FrameAverageModuleTest.BasicTest (1 ms) 67: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 67: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 67: [----------] 2 tests from FrameAverageModuleTest (2 ms total) 67: 67: [----------] 7 tests from AnalysisHistogramSettingsTest 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 67: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 67: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 67: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 67: 67: [----------] 2 tests from SimpleHistogramModuleTest 67: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 67: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (1 ms) 67: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 67: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 67: [----------] 2 tests from SimpleHistogramModuleTest (3 ms total) 67: 67: [----------] 3 tests from WeightedHistogramModuleTest 67: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 67: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (1 ms) 67: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 67: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 67: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 67: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (1 ms) 67: [----------] 3 tests from WeightedHistogramModuleTest (4 ms total) 67: 67: [----------] 3 tests from BinAverageModuleTest 67: [ RUN ] BinAverageModuleTest.ComputesCorrectly 67: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 67: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 67: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (1 ms) 67: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 67: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (1 ms) 67: [----------] 3 tests from BinAverageModuleTest (4 ms total) 67: 67: [----------] 4 tests from AbstractAverageHistogramTest 67: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 67: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (1 ms) 67: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 67: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 67: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 67: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 67: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 67: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (1 ms) 67: [----------] 4 tests from AbstractAverageHistogramTest (6 ms total) 67: 67: [----------] 3 tests from LifetimeModuleTest 67: [ RUN ] LifetimeModuleTest.BasicTest 67: [ OK ] LifetimeModuleTest.BasicTest (1 ms) 67: [ RUN ] LifetimeModuleTest.CumulativeTest 67: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 67: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 67: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (1 ms) 67: [----------] 3 tests from LifetimeModuleTest (3 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 69 tests from 14 test suites ran. (99 ms total) 67: [ PASSED ] 69 tests. 67/103 Test #67: AnalysisDataUnitTests ..................... Passed 0.13 sec test 68 Start 68: CoordinateIOTests 68: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/coordinateio/tests 68: Test timeout computed to be: 30 68: [==========] Running 67 tests from 20 test suites. 68: [----------] Global test environment set-up. 68: [----------] 1 test from OutputSelectorDeathTest 68: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (6 ms) 68: [----------] 1 test from OutputSelectorDeathTest (6 ms total) 68: 68: [----------] 5 tests from TrajectoryFrameWriterTest 68: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (3 ms) 68: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (2 ms) 68: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (2 ms) 68: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (5 ms) 68: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 68: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 68: [----------] 5 tests from TrajectoryFrameWriterTest (14 ms total) 68: 68: [----------] 5 tests from OutputAdapterContainer 68: [ RUN ] OutputAdapterContainer.MakeEmpty 68: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 68: [ RUN ] OutputAdapterContainer.AddAdapter 68: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 68: [ RUN ] OutputAdapterContainer.RejectBadAdapter 68: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 68: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 68: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 68: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 68: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 68: [----------] 5 tests from OutputAdapterContainer (0 ms total) 68: 68: [----------] 3 tests from RegisterFrameConverterTest 68: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 68: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 68: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 68: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 68: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 68: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 68: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 68: 68: [----------] 5 tests from FlagTest 68: [ RUN ] FlagTest.CanSetSimpleFlag 68: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 68: [ RUN ] FlagTest.CanAddNewBox 68: [ OK ] FlagTest.CanAddNewBox (0 ms) 68: [ RUN ] FlagTest.SetsImplicitPrecisionChange 68: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 68: [ RUN ] FlagTest.SetsImplicitStartTimeChange 68: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 68: [ RUN ] FlagTest.SetsImplicitTimeStepChange 68: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 68: [----------] 5 tests from FlagTest (0 ms total) 68: 68: [----------] 5 tests from SetAtomsTest 68: [ RUN ] SetAtomsTest.RemovesExistingAtoms 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] SetAtomsTest.RemovesExistingAtoms (2 ms) 68: [ RUN ] SetAtomsTest.AddsNewAtoms 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] SetAtomsTest.AddsNewAtoms (2 ms) 68: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (2 ms) 68: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (2 ms) 68: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (2 ms) 68: [----------] 5 tests from SetAtomsTest (14 ms total) 68: 68: [----------] 2 tests from SetBothTimeTest 68: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 68: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 68: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 68: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 68: [----------] 2 tests from SetBothTimeTest (0 ms total) 68: 68: [----------] 2 tests from SetStartTimeTest 68: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 68: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 68: [ RUN ] SetStartTimeTest.WorksWithZeroStart 68: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 68: [----------] 2 tests from SetStartTimeTest (0 ms total) 68: 68: [----------] 1 test from SetTimeStepTest 68: [ RUN ] SetTimeStepTest.SetTimeStepWorks 68: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 68: [----------] 1 test from SetTimeStepTest (0 ms total) 68: 68: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (2 ms) 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (2 ms) 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (2 ms) 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (2 ms) 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (2 ms) 68: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (2 ms) 68: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (17 ms total) 68: 68: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 68: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (2 ms) 68: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (2 ms) 68: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (2 ms) 68: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (8 ms total) 68: 68: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 68: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 68: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 68: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 68: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 68: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 68: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 68: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 68: 68: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 68: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (6 ms) 68: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (6 ms) 68: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (6 ms) 68: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (6 ms) 68: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (26 ms total) 68: 68: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 68: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (3 ms) 68: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (3 ms) 68: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (2 ms) 68: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (10 ms total) 68: 68: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 68: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 68: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 68: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 68: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 68: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 68: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 68: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 68: 68: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 68: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (2 ms) 68: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (2 ms) 68: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (5 ms total) 68: 68: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 68: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 68: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 68: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 68: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 68: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 68: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 68: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 68: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 68: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 68: 68: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 68: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (2 ms) 68: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (2 ms) 68: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (5 ms total) 68: 68: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 68: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 68: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 68: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 68: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 68: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 68: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 68: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 68: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 68: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 68: 68: [----------] 4 tests from ModuleSupported/NoOptionalOutput 68: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (2 ms) 68: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (2 ms) 68: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (2 ms) 68: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 68: 68: WARNING: Masses and atomic (Van der Waals) radii will be guessed 68: based on residue and atom names, since they could not be 68: definitively assigned from the information in your input 68: files. These guessed numbers might deviate from the mass 68: and radius of the atom type. Please check the output 68: files if necessary. Note, that this functionality may 68: be removed in a future GROMACS version. Please, consider 68: using another file format for your input. 68: 68: The atomic radii are set according to: 68: 68: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 68: A. Bondi 68: van der Waals Volumes and Radii 68: J. Phys. Chem. (1964) 68: https://doi.org/10.1021/j100785a001 68: -------- -------- --- Thank You --- -------- -------- 68: 68: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (2 ms) 68: [----------] 4 tests from ModuleSupported/NoOptionalOutput (11 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 67 tests from 20 test suites ran. (125 ms total) 68: [ PASSED ] 67 tests. 68/103 Test #68: CoordinateIOTests ......................... Passed 0.15 sec test 69 Start 69: TrajectoryAnalysisUnitTests 69: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests 69: Test timeout computed to be: 1920 69: [==========] Running 394 tests from 21 test suites. 69: [----------] Global test environment set-up. 69: [----------] 11 tests from AngleModuleTest 69: [ RUN ] AngleModuleTest.ComputesSimpleAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesSimpleAngles (4 ms) 69: [ RUN ] AngleModuleTest.ComputesDihedrals 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesDihedrals (3 ms) 69: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesVectorPairAngles (3 ms) 69: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (3 ms) 69: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (3 ms) 69: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (3 ms) 69: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system for different angles', 33 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (4 ms) 69: [ RUN ] AngleModuleTest.ComputesMultipleAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.ComputesMultipleAngles (3 ms) 69: [ RUN ] AngleModuleTest.HandlesDynamicSelections 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.HandlesDynamicSelections (3 ms) 69: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (3 ms) 69: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (3 ms) 69: [----------] 11 tests from AngleModuleTest (41 ms total) 69: 69: [----------] 5 tests from ClustsizeTest 69: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 69: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 69: There is one group in the index 69: '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Total number of atoms in clusters = 24 69: cmid: 2, cmax: 4, max_size: 6 69: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 69: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (3 ms) 69: [ RUN ] ClustsizeTest.NoMolShortCutoff 69: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 69: There is one group in the index 69: '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Total number of atoms in clusters = 24 69: cmid: 1, cmax: 6, max_size: 6 69: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 69: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (3 ms) 69: [ RUN ] ClustsizeTest.MolDefaultCutoff 69: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Total number of atoms in clusters = 8 69: cmid: 2, cmax: 4, max_size: 2 69: 50%100%cmid: 2, cmax: 6, max_size: 2 69: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (18 ms) 69: [ RUN ] ClustsizeTest.MolShortCutoff 69: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Total number of atoms in clusters = 8 69: cmid: 1, cmax: 6, max_size: 2 69: 50%100%cmid: 2, cmax: 6, max_size: 2 69: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (4 ms) 69: [ RUN ] ClustsizeTest.MolCSize 69: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Total number of atoms in clusters = 8 69: cmid: 2, cmax: 4, max_size: 2 69: 50%100%cmid: 2, cmax: 6, max_size: 2 69: 50%100%[ OK ] ClustsizeTest.MolCSize (5 ms) 69: [----------] 5 tests from ClustsizeTest (34 ms total) 69: 69: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 69: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 69: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (1 ms) 69: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 8 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (3 ms) 69: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 8 atoms. 69: Reading frame 0 time 0.000 [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (3 ms) 69: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 69: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 69: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (8 ms total) 69: 69: [----------] 4 tests from ConvertTrjModuleTest 69: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (16 ms) 69: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (16 ms) 69: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (3 ms) 69: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 69: Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (3 ms) 69: [----------] 4 tests from ConvertTrjModuleTest (39 ms total) 69: 69: [----------] 6 tests from DistanceModuleTest 69: [ RUN ] DistanceModuleTest.ComputesDistances 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: atomname S1 S2: 69: Number of samples: 5 69: Average distance: 1.43246 nm 69: Standard deviation: 0.96700 nm 69: [ OK ] DistanceModuleTest.ComputesDistances (5 ms) 69: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: atomname S1 S2: 69: Number of samples: 5 69: Average distance: 1.43246 nm 69: Standard deviation: 0.96700 nm 69: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 69: Number of samples: 4 69: Average distance: 1.81066 nm 69: Standard deviation: 0.79289 nm 69: [ OK ] DistanceModuleTest.ComputesMultipleDistances (4 ms) 69: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: atomname S1 S2 and res_cog x < 2.8: 69: Number of samples: 3 69: Average distance: 1.72076 nm 69: Standard deviation: 1.24839 nm 69: [ OK ] DistanceModuleTest.HandlesDynamicSelections (4 ms) 69: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: Contacts: 69: Number of samples: 2 69: Average distance: 1.00000 nm 69: Standard deviation: 0.00000 nm 69: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (11 ms) 69: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: SuccessiveContacts: 69: Number of samples: 2 69: Average distance: 1.00000 nm 69: Standard deviation: 0.00000 nm 69: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (12 ms) 69: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: ManyContacts: 69: Number of samples: 10 69: Average distance: 1.82913 nm 69: Standard deviation: 0.78478 nm 69: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (14 ms) 69: [----------] 6 tests from DistanceModuleTest (55 ms total) 69: 69: [----------] 2 tests from ExtractClusterModuleTest 69: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 69: trr version: GMX_trn_file (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 69: Analyzed 26 frames, last time 0.050 69: There are 8 clusters containing 26 structures, highest framenr is 25 69: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (5 ms) 69: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 69: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 69: Analyzed 26 frames, last time 0.050 69: There are 8 clusters containing 26 structures, highest framenr is 25 69: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (4 ms) 69: [----------] 2 tests from ExtractClusterModuleTest (10 ms total) 69: 69: [----------] 2 tests from FreeVolumeModuleTest 69: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for CO2-RM. Set to zero. 69: Could not determine VDW radius for 40 particles. These were set to zero. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: cutoff = 0.18 nm 69: probe_radius = 0 nm 69: seed = 13 69: ninsert = 1000 probes per nm^3 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 69: Spoel, Luciano T. Costa 69: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 69: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 69: Environ. Sci. Technol. (2013) 69: https://doi.org/10.1021/es4020986 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Free volume 38.02 +/- 0.00 % 69: Total volume 68.92 +/- 0.00 nm^3 69: Number of molecules 340 total mass 63491.38 Dalton 69: Average molar mass: 186.74 Dalton 69: Density rho: 1529.71 +/- 0.00 nm^3 69: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 69: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 69: Fractional free volume 0.194 +/- 0.000 69: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (149 ms) 69: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: cutoff = 0.18 nm 69: probe_radius = 0 nm 69: seed = 17 69: ninsert = 1000 probes per nm^3 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Tuanan C. Lourenco, Mariny F. C. Coelho, Teodorico C. Ramalho, David van der 69: Spoel, Luciano T. Costa 69: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 69: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 69: Environ. Sci. Technol. (2013) 69: https://doi.org/10.1021/es4020986 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Free volume 38.48 +/- 0.00 % 69: Total volume 68.92 +/- 0.00 nm^3 69: Number of molecules 340 total mass 63491.38 Dalton 69: Average molar mass: 186.74 Dalton 69: Density rho: 1529.71 +/- 0.00 nm^3 69: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 69: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 69: Fractional free volume 0.200 +/- 0.000 69: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (191 ms) 69: [----------] 2 tests from FreeVolumeModuleTest (341 ms total) 69: 69: [----------] 13 tests from MsdModuleTest 69: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 69: Analyzed 10 frames, last time 9.000 69: [ OK ] MsdModuleTest.threeDimensionalDiffusion (48 ms) 69: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 69: Analyzed 10 frames, last time 9.000 69: [ OK ] MsdModuleTest.twoDimensionalDiffusion (4 ms) 69: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 69: Analyzed 10 frames, last time 9.000 69: [ OK ] MsdModuleTest.oneDimensionalDiffusion (4 ms) 69: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 69: Analyzed 10 frames, last time 9.000 69: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (4 ms) 69: [ RUN ] MsdModuleTest.multipleGroupsWork 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 69: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 69: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to -134286599 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.multipleGroupsWork (48 ms) 69: [ RUN ] MsdModuleTest.subPicosecondTrajectoryWorks 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_subPicosecondTrajectoryWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 0.100 69: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 69: Reading frame 2 time 0.200 Reading frame 3 time 0.300 Reading frame 4 time 0.400 Reading frame 5 time 0.500 Reading frame 6 time 0.600 Reading frame 7 time 0.700 Reading frame 8 time 0.800 Reading frame 9 time 0.900 Reading frame 10 time 1.000 Reading frame 11 time 1.100 Reading frame 12 time 1.200 Reading frame 13 time 1.300 Reading frame 14 time 1.400 Reading frame 15 time 1.500 Reading frame 16 time 1.600 Reading frame 17 time 1.700 Reading frame 18 time 1.800 Reading frame 19 time 1.900 Reading frame 20 time 2.000 Last frame 20 time 2.000 69: Analyzed 21 frames, last time 2.000 69: Setting the LD random seed to -671107125 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.subPicosecondTrajectoryWorks (48 ms) 69: [ RUN ] MsdModuleTest.trestartLessThanDt 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -705766217 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.trestartLessThanDt (39 ms) 69: [ RUN ] MsdModuleTest.trestartGreaterThanDt 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to -100688915 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.trestartGreaterThanDt (45 ms) 69: [ RUN ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDtAndNotAMultipleOfDt.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Setting the LD random seed to -1173531 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.trestartGreaterThanDtAndNotAMultipleOfDt (39 ms) 69: [ RUN ] MsdModuleTest.molTest 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to -25362961 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.molTest (43 ms) 69: [ RUN ] MsdModuleTest.beginFit 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 69: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 69: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to -302289937 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.beginFit (42 ms) 69: [ RUN ] MsdModuleTest.endFit 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 69: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 69: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to -1241530625 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.endFit (42 ms) 69: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 69: For energy conservation with LINCS, lincs_iter should be 2 or larger. 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 1818.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 69: NVE simulation: will use the initial temperature of 288.764 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: NOTE: You provided an index file 69: /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 69: (with -n), but it was not used by any selection. 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 2.000 69: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 69: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 69: Analyzed 21 frames, last time 40.000 69: Setting the LD random seed to -1375753665 69: 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_solvated.gro' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Converted 15 Bonds with virtual sites to connections, 7 left 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (44 ms) 69: [----------] 13 tests from MsdModuleTest (458 ms total) 69: 69: [----------] 9 tests from PairDistanceModuleTest 69: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesAllDistances (3 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (3 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (4 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (3 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (3 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (3 ms) 69: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (3 ms) 69: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (3 ms) 69: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (3 ms) 69: [----------] 9 tests from PairDistanceModuleTest (32 ms total) 69: 69: [----------] 5 tests from RdfModuleTest 69: [ RUN ] RdfModuleTest.BasicTest 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] RdfModuleTest.BasicTest (42 ms) 69: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 69: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 69: Reading frame 0 time 0.000 Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (39 ms) 69: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (42 ms) 69: [ RUN ] RdfModuleTest.CalculatesSurf 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] RdfModuleTest.CalculatesSurf (14 ms) 69: [ RUN ] RdfModuleTest.CalculatesXY 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] RdfModuleTest.CalculatesXY (92 ms) 69: [----------] 5 tests from RdfModuleTest (233 ms total) 69: 69: [----------] 5 tests from SasaModuleTest 69: [ RUN ] SasaModuleTest.BasicTest 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 69: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 69: of Surface Area and Volume and to Dot Surface Contouring of Molecular 69: Assemblies 69: J. Comp. Chem. (1995) 69: https://doi.org/10.1002/jcc.540160303 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SasaModuleTest.BasicTest (18 ms) 69: [ RUN ] SasaModuleTest.HandlesSelectedResidues 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 69: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 69: of Surface Area and Volume and to Dot Surface Contouring of Molecular 69: Assemblies 69: J. Comp. Chem. (1995) 69: https://doi.org/10.1002/jcc.540160303 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SasaModuleTest.HandlesSelectedResidues (16 ms) 69: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 69: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 69: of Surface Area and Volume and to Dot Surface Contouring of Molecular 69: Assemblies 69: J. Comp. Chem. (1995) 69: https://doi.org/10.1002/jcc.540160303 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (6 ms) 69: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 69: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 69: of Surface Area and Volume and to Dot Surface Contouring of Molecular 69: Assemblies 69: J. Comp. Chem. (1995) 69: https://doi.org/10.1002/jcc.540160303 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (11 ms) 69: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf 69: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 69: of Surface Area and Volume and to Dot Surface Contouring of Molecular 69: Assemblies 69: J. Comp. Chem. (1995) 69: https://doi.org/10.1002/jcc.540160303 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (11 ms) 69: [----------] 5 tests from SasaModuleTest (66 ms total) 69: 69: [----------] 9 tests from SelectModuleTest 69: [ RUN ] SelectModuleTest.BasicTest 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] SelectModuleTest.BasicTest (7 ms) 69: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (3 ms) 69: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (3 ms) 69: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (4 ms) 69: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (4 ms) 69: [ RUN ] SelectModuleTest.NormalizesSizes 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SelectModuleTest.NormalizesSizes (3 ms) 69: [ RUN ] SelectModuleTest.WritesResidueNumbers 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SelectModuleTest.WritesResidueNumbers (4 ms) 69: [ RUN ] SelectModuleTest.WritesResidueIndices 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SelectModuleTest.WritesResidueIndices (2 ms) 69: [ RUN ] SelectModuleTest.HandlesPrimeInAtomName 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Analyzed topology coordinates 69: [ OK ] SelectModuleTest.HandlesPrimeInAtomName (3 ms) 69: [----------] 9 tests from SelectModuleTest (37 ms total) 69: 69: [----------] 10 tests from SurfaceAreaTest 69: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 69: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 69: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 69: [ OK ] SurfaceAreaTest.ComputesTwoPoints (2 ms) 69: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 69: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (2 ms) 69: [ RUN ] SurfaceAreaTest.SurfacePoints12 69: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 69: [ RUN ] SurfaceAreaTest.SurfacePoints32 69: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 69: [ RUN ] SurfaceAreaTest.SurfacePoints42 69: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 69: [ RUN ] SurfaceAreaTest.SurfacePoints122 69: [ OK ] SurfaceAreaTest.SurfacePoints122 (2 ms) 69: [ RUN ] SurfaceAreaTest.Computes100Points 69: [ OK ] SurfaceAreaTest.Computes100Points (1 ms) 69: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 69: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (6 ms) 69: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 69: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (6 ms) 69: [----------] 10 tests from SurfaceAreaTest (23 ms total) 69: 69: [----------] 4 tests from TopologyInformation 69: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 69: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 69: [ RUN ] TopologyInformation.WorksWithGroFile 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TopologyInformation.WorksWithGroFile (2 ms) 69: [ RUN ] TopologyInformation.WorksWithPdbFile 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] TopologyInformation.WorksWithPdbFile (2 ms) 69: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 69: For a correct single-point energy evaluation with nsteps = 0, use 69: continuation = yes to avoid constraining the input coordinates. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 2 [file lysozyme.top, line 1465]: 69: System has non-zero total charge: 2.000000 69: Total charge should normally be an integer. See 69: https://manual.gromacs.org/current/user-guide/floating-point.html 69: for discussion on how close it should be to an integer. 69: 69: 69: 69: Number of degrees of freedom in T-Coupling group rest is 465.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 69: NVE simulation with an initial temperature of zero: will use a Verlet 69: buffer of 10%. Check your energy drift! 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 69: Setting the LD random seed to -1074806913 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 69: 69: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 69: Analysing residue names: 69: There are: 10 Protein residues 69: Analysing Protein... 69: 69: This run will generate roughly 0 Mb of data 69: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (1035 ms) 69: [----------] 4 tests from TopologyInformation (1041 ms total) 69: 69: [----------] 4 tests from TrajectoryModuleTest 69: [ RUN ] TrajectoryModuleTest.BasicTest 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] TrajectoryModuleTest.BasicTest (4 ms) 69: [ RUN ] TrajectoryModuleTest.PlotsXOnly 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] TrajectoryModuleTest.PlotsXOnly (3 ms) 69: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (3 ms) 69: [ RUN ] TrajectoryModuleTest.HandlesNoForces 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from gro file 'Test system', 15 atoms. 69: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 69: Analyzed 2 frames, last time 0.000 69: [ OK ] TrajectoryModuleTest.HandlesNoForces (3 ms) 69: [----------] 4 tests from TrajectoryModuleTest (14 ms total) 69: 69: [----------] 5 tests from UnionFinderTest 69: [ RUN ] UnionFinderTest.WorksEmpty 69: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 69: [ RUN ] UnionFinderTest.BasicMerges 69: [ OK ] UnionFinderTest.BasicMerges (0 ms) 69: [ RUN ] UnionFinderTest.LargerMerges 69: [ OK ] UnionFinderTest.LargerMerges (0 ms) 69: [ RUN ] UnionFinderTest.LongRightMerge 69: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 69: [ RUN ] UnionFinderTest.LongLeftMerge 69: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 69: [----------] 5 tests from UnionFinderTest (0 ms total) 69: 69: [----------] 1 test from MappedUnionFinderTest 69: [ RUN ] MappedUnionFinderTest.BasicMerges 69: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 69: [----------] 1 test from MappedUnionFinderTest (0 ms total) 69: 69: [----------] 192 tests from MoleculeTests/DsspModuleTest 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/0 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/1 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/2 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/2 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/3 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/3 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/4 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/4 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/5 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/5 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/6 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/6 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/7 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/7 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/8 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/8 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/9 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/9 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/10 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/10 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/11 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/11 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/12 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/12 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/13 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/13 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/14 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/14 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/15 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/15 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/16 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/16 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/17 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/17 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/18 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/18 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/19 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/19 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/20 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/20 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/21 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/21 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/22 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/22 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/23 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/23 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/24 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/24 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/25 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/25 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/26 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/26 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/27 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/27 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/28 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/28 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/29 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/29 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/30 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/30 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/31 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/31 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/32 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/32 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/33 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/33 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/34 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/34 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/35 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/35 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/36 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/36 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/37 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/37 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/38 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/38 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/39 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/39 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/40 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/40 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/41 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/41 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/42 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/42 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/43 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/43 (43 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/44 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/44 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/45 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/45 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/46 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/46 (44 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/47 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/47 (44 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/48 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/48 (44 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/49 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/49 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/50 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/50 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/51 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/51 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/52 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/52 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/53 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/53 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/54 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/54 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/55 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/55 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/56 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/56 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/57 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/57 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/58 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/58 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/59 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/59 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/60 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/60 (41 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/61 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/61 (44 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/62 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/62 (44 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/63 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 2092 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/63 (42 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/64 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/64 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/65 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/65 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/66 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/66 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/67 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/67 (40 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/68 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/68 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/69 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/69 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/70 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/70 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/71 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/71 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/72 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/72 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/73 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/73 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/74 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/74 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/75 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/75 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/76 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/76 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/77 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/77 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/78 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/78 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/79 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/79 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/80 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/80 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/81 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/81 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/82 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/82 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/83 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/83 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/84 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/84 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/85 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/85 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/86 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/86 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/87 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/87 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/88 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/88 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/89 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/89 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/90 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/90 (78 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/91 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/91 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/92 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/92 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/93 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/93 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/94 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/94 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/95 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/95 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/96 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/96 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/97 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/97 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/98 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/98 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/99 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/99 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/100 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/100 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/101 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/101 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/102 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/102 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/103 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/103 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/104 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/104 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/105 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/105 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/106 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/106 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/107 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/107 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/108 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/108 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/109 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/109 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/110 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/110 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/111 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/111 (39 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/112 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/112 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/113 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/113 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/114 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/114 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/115 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/115 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/116 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/116 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/117 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/117 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/118 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/118 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/119 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/119 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/120 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/120 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/121 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/121 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/122 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/122 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/123 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/123 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/124 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/124 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/125 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/125 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/126 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/126 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/127 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/127 (38 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/128 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/128 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/129 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/129 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/130 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/130 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/131 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/131 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/132 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/132 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/133 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/133 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/134 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/134 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/135 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/135 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/136 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/136 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/137 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/137 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/138 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/138 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/139 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/139 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/140 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/140 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/141 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/141 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/142 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/142 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/143 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/143 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/144 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/144 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/145 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/145 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/146 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/146 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/147 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/147 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/148 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/148 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/149 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/149 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/150 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/150 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/151 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/151 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/152 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/152 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/153 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/153 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/154 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/154 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/155 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/155 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/156 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/156 (31 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/157 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/157 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/158 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/158 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/159 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/159 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/160 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/160 (66 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/161 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/161 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/162 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/162 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/163 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/163 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/164 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/164 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/165 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/165 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/166 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/166 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/167 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/167 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/168 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/168 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/169 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/169 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/170 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/170 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/171 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/171 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/172 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/172 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/173 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/173 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/174 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/174 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/175 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/175 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/176 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/176 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/177 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/177 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/178 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/178 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/179 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/179 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/180 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/180 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/181 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/181 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/182 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/182 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/183 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/183 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/184 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/184 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/185 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/185 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/186 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/186 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/187 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/187 (30 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/188 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/188 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/189 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/189 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/190 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/190 (29 ms) 69: [ RUN ] MoleculeTests/DsspModuleTest.Works/191 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 69: Last frame 0 time 500.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: W. Kabsch, C. Sander 69: Dictionary of protein secondary structure: pattern recognition of 69: hydrogen-bonded and geometrical features 69: Biopolymers (1983) 69: https://doi.org/10.1002/bip.360221211 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 69: Trajectories 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c01344 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/DsspModuleTest.Works/191 (29 ms) 69: [----------] 192 tests from MoleculeTests/DsspModuleTest (7215 ms total) 69: 69: [----------] 3 tests from GyrateTests/GyrateModuleTest 69: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (14 ms) 69: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (14 ms) 69: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (14 ms) 69: [----------] 3 tests from GyrateTests/GyrateModuleTest (42 ms total) 69: 69: [----------] 96 tests from HBondTests/HbondModuleTest 69: [ RUN ] HBondTests/HbondModuleTest.Works/0 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/0 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/1 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/1 (26 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/2 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/2 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/3 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/3 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/4 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/4 (26 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/5 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/5 (61 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/6 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/6 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/7 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/7 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/8 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/8 (26 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/9 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/9 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/10 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/10 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/11 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/11 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/12 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/12 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/13 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/13 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/14 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/14 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/15 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/15 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/16 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/16 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/17 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/17 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/18 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/18 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/19 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/19 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/20 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/20 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/21 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/21 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/22 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/22 (24 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/23 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/23 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/24 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/24 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/25 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/25 (76 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/26 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/26 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/27 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/27 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/28 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/28 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/29 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/29 (25 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/30 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/30 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/31 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/31 (23 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/32 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/32 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/33 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/33 (157 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/34 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/34 (236 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/35 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/35 (159 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/36 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/36 (198 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/37 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/37 (155 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/38 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/38 (194 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/39 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/39 (189 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/40 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/40 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/41 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/41 (194 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/42 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/42 (196 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/43 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/43 (194 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/44 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/44 (194 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/45 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/45 (192 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/46 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/46 (159 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/47 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/47 (154 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/48 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/48 (198 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/49 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/49 (192 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/50 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/50 (193 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/51 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/51 (191 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/52 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/52 (194 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/53 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/53 (193 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/54 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/54 (194 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/55 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/55 (190 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/56 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/56 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/57 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/57 (198 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/58 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/58 (160 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/59 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/59 (229 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/60 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/60 (162 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/61 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 27 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/61 (191 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/62 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 56 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/62 (195 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/63 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 69: Selection 'Protein' has 29 acceptors and 4 donors. 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Merging hbonds with Acceptor and Donor swapped 69: [ OK ] HBondTests/HbondModuleTest.Works/63 (190 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/64 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/64 (179 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/65 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/65 (177 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/66 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/66 (177 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/67 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/67 (178 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/68 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/68 (189 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/69 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/69 (169 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/70 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/70 (188 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/71 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/71 (186 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/72 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/72 (196 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/73 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/73 (195 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/74 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/74 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/75 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/75 (199 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/76 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/76 (196 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/77 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/77 (196 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/78 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/78 (158 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/79 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/79 (198 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/80 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/80 (231 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/81 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/81 (140 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/82 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/82 (176 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/83 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/83 (174 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/84 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/84 (187 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/85 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/85 (186 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/86 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/86 (185 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/87 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/87 (187 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/88 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/88 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/89 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/89 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/90 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/90 (162 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/91 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/91 (198 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/92 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/92 (196 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/93 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/93 (166 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/94 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/94 (197 ms) 69: [ RUN ] HBondTests/HbondModuleTest.Works/95 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 69: Analyzed 2 frames, last time 10.000 69: 69: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 69: Selection 'Water' has 1160 acceptors and 1160 donors. 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 69: Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome 69: Memory Limitation 69: Journal of Chemical Information and Modeling (2024) 69: https://doi.org/10.1021/acs.jcim.3c02087 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] HBondTests/HbondModuleTest.Works/95 (195 ms) 69: [----------] 96 tests from HBondTests/HbondModuleTest (14844 ms total) 69: 69: [----------] 4 tests from MoleculeTests/ScatteringModule 69: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 69: Method for calculating small-angle neutron scattering spectra using all-atom 69: molecular dynamics trajectories 69: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 69: https://doi.org/10.1134/S1027451013060372 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (21 ms) 69: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 69: Method for calculating small-angle neutron scattering spectra using all-atom 69: molecular dynamics trajectories 69: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 69: https://doi.org/10.1134/S1027451013060372 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: D. T. Cromer, J. B. Mann 69: X-ray scattering factors computed from numerical Hartree-Fock wave functions 69: Acta Cryst. A (1968) 69: https://doi.org/10.1107/S0567739468000550 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (665 ms) 69: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 69: Method for calculating small-angle neutron scattering spectra using all-atom 69: molecular dynamics trajectories 69: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 69: https://doi.org/10.1134/S1027451013060372 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (53 ms) 69: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 69: 69: WARNING: Masses and atomic (Van der Waals) radii will be guessed 69: based on residue and atom names, since they could not be 69: definitively assigned from the information in your input 69: files. These guessed numbers might deviate from the mass 69: and radius of the atom type. Please check the output 69: files if necessary. Note, that this functionality may 69: be removed in a future GROMACS version. Please, consider 69: using another file format for your input. 69: 69: The atomic radii are set according to: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. Bondi 69: van der Waals Volumes and Radii 69: J. Phys. Chem. (1964) 69: https://doi.org/10.1021/j100785a001 69: -------- -------- --- Thank You --- -------- -------- 69: 69: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 69: Last frame 0 time 0.000 69: Analyzed 1 frames, last time 0.000 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev, V. V. Isaev-Ivanov 69: Method for calculating small-angle neutron scattering spectra using all-atom 69: molecular dynamics trajectories 69: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques (2013) 69: https://doi.org/10.1134/S1027451013060372 69: -------- -------- --- Thank You --- -------- -------- 69: 69: 69: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 69: D. T. Cromer, J. B. Mann 69: X-ray scattering factors computed from numerical Hartree-Fock wave functions 69: Acta Cryst. A (1968) 69: https://doi.org/10.1107/S0567739468000550 69: -------- -------- --- Thank You --- -------- -------- 69: 69: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (151 ms) 69: [----------] 4 tests from MoleculeTests/ScatteringModule (898 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 394 tests from 21 test suites ran. (25441 ms total) 69: [ PASSED ] 394 tests. 69/103 Test #69: TrajectoryAnalysisUnitTests ............... Passed 25.50 sec test 70 Start 70: EnergyAnalysisUnitTests 70: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests 70: Test timeout computed to be: 30 70: [==========] Running 12 tests from 5 test suites. 70: [----------] Global test environment set-up. 70: [----------] 2 tests from EnergyTermTest 70: [ RUN ] EnergyTermTest.ConstructWorks 70: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 70: [ RUN ] EnergyTermTest.AddFrameWorks 70: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 70: [----------] 2 tests from EnergyTermTest (0 ms total) 70: 70: [----------] 1 test from DhdlTest 70: [ RUN ] DhdlTest.ExtractDhdl 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 70: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 70: Note: file tpx version 110, software tpx version 138 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 70: 70: 70: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 70: [ OK ] DhdlTest.ExtractDhdl (50 ms) 70: [----------] 1 test from DhdlTest (51 ms total) 70: 70: [----------] 1 test from OriresTest 70: [ RUN ] OriresTest.ExtractOrires 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 70: Reading file /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 70: Note: file tpx version 111, software tpx version 138 70: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 70: End your selection with 0 70: Selecting all 7 orientation restraints 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 70: [ OK ] OriresTest.ExtractOrires (18 ms) 70: [----------] 1 test from OriresTest (18 ms total) 70: 70: [----------] 5 tests from EnergyTest 70: [ RUN ] EnergyTest.ExtractEnergy 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: 70: Select the terms you want from the following list by 70: selecting either (part of) the name or the number or a combination. 70: End your selection with an empty line or a zero. 70: ------------------------------------------------------------------- 70: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 70: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 70: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 70: 13 Box-Z 14 Volume 15 Density 16 pV 70: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 70: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 70: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 70: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 70: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 70: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 70: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 70: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 70: [ OK ] EnergyTest.ExtractEnergy (3 ms) 70: [ RUN ] EnergyTest.ExtractEnergyByNumber 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: 70: Select the terms you want from the following list by 70: selecting either (part of) the name or the number or a combination. 70: End your selection with an empty line or a zero. 70: ------------------------------------------------------------------- 70: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 70: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 70: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 70: 13 Box-Z 14 Volume 15 Density 16 pV 70: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 70: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 70: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 70: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 70: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 70: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 70: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 70: Pres. DC -268.49 3 8.52175 13.2804 (bar) 70: [ OK ] EnergyTest.ExtractEnergyByNumber (3 ms) 70: [ RUN ] EnergyTest.ExtractEnergyMixed 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: 70: Select the terms you want from the following list by 70: selecting either (part of) the name or the number or a combination. 70: End your selection with an empty line or a zero. 70: ------------------------------------------------------------------- 70: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 70: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 70: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 70: 13 Box-Z 14 Volume 15 Density 16 pV 70: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 70: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 70: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 70: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 70: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 70: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 70: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 70: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 70: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 70: [ OK ] EnergyTest.ExtractEnergyMixed (4 ms) 70: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 70: 70: Select the terms you want from the following list by 70: selecting either (part of) the name or the number or a combination. 70: End your selection with an empty line or a zero. 70: ------------------------------------------------------------------- 70: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 70: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 70: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 70: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 70: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 70: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 70: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 70: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 70: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 70: 37 1/Viscosity 38 T-System 39 Lamb-System 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 70: 70: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 70: All statistics are over 3 points (frames) 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 70: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (1 ms) 70: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 70: 70: Select the terms you want from the following list by 70: selecting either (part of) the name or the number or a combination. 70: End your selection with an empty line or a zero. 70: ------------------------------------------------------------------- 70: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 70: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 70: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 70: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 70: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 70: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 70: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 70: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 70: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 70: 37 1/Viscosity 38 T-System 39 Lamb-System 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 70: 70: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 70: All statistics are over 3 points (frames) 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 70: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 70: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (1 ms) 70: [----------] 5 tests from EnergyTest (15 ms total) 70: 70: [----------] 3 tests from ViscosityTest 70: [ RUN ] ViscosityTest.EinsteinViscosity 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Pres-XX 20.2092 65 717.193 185.978 (bar) 70: Pres-XY -47.7351 39 372.522 207.456 (bar) 70: Pres-XZ 11.477 31 379.79 6.80818 (bar) 70: Pres-YX -47.7106 39 372.525 207.5 (bar) 70: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 70: Pres-YZ -41.3534 45 401.216 114.663 (bar) 70: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 70: Pres-ZY -41.3119 45 401.196 114.743 (bar) 70: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 70: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 70: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 70: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 70: 70: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 70: [ OK ] ViscosityTest.EinsteinViscosity (24 ms) 70: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Pres-XX 20.2092 65 717.193 185.978 (bar) 70: Pres-XY -47.7351 39 372.522 207.456 (bar) 70: Pres-XZ 11.477 31 379.79 6.80818 (bar) 70: Pres-YX -47.7106 39 372.525 207.5 (bar) 70: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 70: Pres-YZ -41.3534 45 401.216 114.663 (bar) 70: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 70: Pres-ZY -41.3119 45 401.196 114.743 (bar) 70: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 70: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 70: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 70: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 70: 70: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 70: [ OK ] ViscosityTest.EinsteinViscosityIntegral (9 ms) 70: [ RUN ] ViscosityTest.EinsteinViscosityDefaultArguments 70: Opened /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 70: 70: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 70: All statistics are over 5001 points 70: 70: Energy Average Err.Est. RMSD Tot-Drift 70: ------------------------------------------------------------------------------- 70: Pres-XX 20.2092 65 717.193 185.978 (bar) 70: Pres-XY -47.7351 39 372.522 207.456 (bar) 70: Pres-XZ 11.477 31 379.79 6.80818 (bar) 70: Pres-YX -47.7106 39 372.525 207.5 (bar) 70: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 70: Pres-YZ -41.3534 45 401.216 114.663 (bar) 70: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 70: Pres-ZY -41.3119 45 401.196 114.743 (bar) 70: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 70: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 70: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 70: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 70: 70: Computing shear viscosity using the Einstein relation with 6 start points separated by 0.2 ps 70: [ OK ] ViscosityTest.EinsteinViscosityDefaultArguments (9 ms) 70: [----------] 3 tests from ViscosityTest (43 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 12 tests from 5 test suites ran. (130 ms total) 70: [ PASSED ] 12 tests. 70/103 Test #70: EnergyAnalysisUnitTests ................... Passed 0.16 sec test 71 Start 71: ToolUnitTests 71: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests 71: Test timeout computed to be: 1920 71: [==========] Running 70 tests from 8 test suites. 71: [----------] Global test environment set-up. 71: [----------] 2 tests from DumpTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Setting the LD random seed to -539241125 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: [ RUN ] DumpTest.WorksWithTpr 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 71: inputrec: 71: integrator = md 71: tinit = 0 71: dt = 0.001 71: nsteps = 0 71: init-step = 0 71: simulation-part = 1 71: mts = false 71: mass-repartition-factor = 1 71: comm-mode = Linear 71: nstcomm = 100 71: bd-fric = 0 71: ld-seed = -539241125 71: emtol = 10 71: emstep = 0.01 71: niter = 20 71: fcstep = 0 71: nstcgsteep = 1000 71: nbfgscorr = 10 71: rtpi = 0.05 71: nstxout = 0 71: nstvout = 0 71: nstfout = 0 71: nstlog = 1000 71: nstcalcenergy = 100 71: nstenergy = 1000 71: nstxout-compressed = 0 71: compressed-x-precision = 1000 71: cutoff-scheme = Verlet 71: nstlist = 10 71: pbc = xyz 71: periodic-molecules = false 71: verlet-buffer-tolerance = -1 71: verlet-buffer-pressure-tolerance = 0.5 71: rlist = 1.1 71: coulombtype = Cut-off 71: coulomb-modifier = Potential-shift 71: rcoulomb-switch = 0 71: rcoulomb = 1 71: epsilon-r = 1 71: epsilon-rf = inf 71: vdw-type = Cut-off 71: vdw-modifier = Potential-shift 71: rvdw-switch = 0 71: rvdw = 1 71: DispCorr = No 71: table-extension = 1 71: fourierspacing = 0.12 71: fourier-nx = 0 71: fourier-ny = 0 71: fourier-nz = 0 71: pme-order = 4 71: ewald-rtol = 1e-05 71: ewald-rtol-lj = 0.001 71: lj-pme-comb-rule = Geometric 71: ewald-geometry = 3d 71: epsilon-surface = 0 71: ensemble-temperature-setting = not available 71: tcoupl = No 71: nsttcouple = -1 71: nh-chain-length = 0 71: print-nose-hoover-chain-variables = false 71: pcoupl = No 71: refcoord-scaling = No 71: posres-com: not available 71: posres-comB: not available 71: QMMM = false 71: qm-opts: 71: ngQM = 0 71: constraint-algorithm = Lincs 71: continuation = false 71: Shake-SOR = false 71: shake-tol = 0.0001 71: lincs-order = 4 71: lincs-iter = 1 71: lincs-warnangle = 30 71: nwall = 0 71: wall-type = 9-3 71: wall-r-linpot = -1 71: wall-atomtype[0] = -1 71: wall-atomtype[1] = -1 71: wall-density[0] = 0 71: wall-density[1] = 0 71: wall-ewald-zfac = 3 71: pull = false 71: awh = false 71: rotation = false 71: interactiveMD = false 71: disre = No 71: disre-weighting = Conservative 71: disre-mixed = false 71: dr-fc = 1000 71: dr-tau = 0 71: nstdisreout = 100 71: orire-fc = 0 71: orire-tau = 0 71: nstorireout = 100 71: free-energy = no 71: cos-acceleration = 0 71: deform (3x3): 71: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: simulated-tempering = false 71: swapcoords = no 71: userint1 = 0 71: userint2 = 0 71: userint3 = 0 71: userint4 = 0 71: userreal1 = 0 71: userreal2 = 0 71: userreal3 = 0 71: userreal4 = 0 71: applied-forces: 71: electric-field: 71: x: 71: E0 = 0 71: omega = 0 71: t0 = 0 71: sigma = 0 71: y: 71: E0 = 0 71: omega = 0 71: t0 = 0 71: sigma = 0 71: z: 71: E0 = 0 71: omega = 0 71: t0 = 0 71: sigma = 0 71: density-guided-simulation: 71: active = false 71: group = protein 71: similarity-measure = inner-product 71: atom-spreading-weight = unity 71: force-constant = 1e+09 71: gaussian-transform-spreading-width = 0.2 71: gaussian-transform-spreading-range-in-multiples-of-width = 4 71: reference-density-filename = reference.mrc 71: nst = 1 71: normalize-densities = true 71: adaptive-force-scaling = false 71: adaptive-force-scaling-time-constant = 4 71: shift-vector = 71: transformation-matrix = 71: qmmm-cp2k: 71: active = false 71: qmgroup = System 71: qmmethod = PBE 71: qmfilenames = 71: qmcharge = 0 71: qmmultiplicity = 1 71: colvars: 71: active = false 71: configfile = 71: seed = -1 71: nnpot: 71: active = false 71: modelfile = model.pt 71: input-group = System 71: link-type = H 71: link-distance = 0.1 71: pair-cutoff = 0 71: embedding = mechanical 71: nnp-charge = 0 71: model-input1 = 71: model-input2 = 71: model-input3 = 71: model-input4 = 71: model-input5 = 71: model-input6 = 71: model-input7 = 71: model-input8 = 71: model-input9 = 71: fast-multipole-method: 71: fmm: 71: backend = inactive 71: exafmm-order = 6 71: exafmm-direct-range = 2 71: exafmm-direct-provider = GROMACS 71: exafmm-tree-type = uniform 71: exafmm-tree-depth = 0 71: exafmm-max-particles-per-cell = 0 71: fmsolvr-order = 8 71: fmsolvr-direct-range = 1 71: fmsolvr-direct-provider = FMM 71: fmsolvr-dipole-compensation = true 71: fmsolvr-tree-depth = 3 71: fmsolvr-sparse = false 71: grpopts: 71: nrdf: 465 71: ref-t: 0 71: tau-t: 0 71: annealing: No 71: annealing-npoints: 0 71: acc: 0 0 0 71: nfreeze: N N N 71: energygrp-flags[ 0]: 0 71: header: 71: bIr = present 71: bBox = present 71: bTop = present 71: bX = present 71: bV = present 71: bF = not present 71: natoms = 156 71: lambda = 0.000000e+00 71: buffer size = 57866 71: topology: 71: name="First 10 residues from 1AKI" 71: #atoms = 156 71: #molblock = 1 71: molblock (0): 71: moltype = 0 "Protein_chain_B" 71: #molecules = 1 71: #posres_xA = 0 71: #posres_xB = 0 71: bIntermolecularInteractions = false 71: ffparams: 71: atnr=10 71: ntypes=212 71: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 71: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 71: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 71: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 71: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 71: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 71: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 71: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 71: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 71: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 71: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 71: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 71: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 71: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 71: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 71: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 71: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 71: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 71: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 71: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 71: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 71: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08 71: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07 71: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07 71: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07 71: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08 71: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08 71: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06 71: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 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0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 71: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 71: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 71: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 71: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 71: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 71: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 71: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 71: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 71: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 71: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 71: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 71: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 71: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 71: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 71: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 71: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 71: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 71: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 71: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 71: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 71: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 71: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 71: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 71: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 71: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 71: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 71: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 71: reppow = 12 71: fudgeQQ = 0.5 71: cmap 71: moltype (0): 71: name="Protein_chain_B" 71: atoms: 71: atom (156): 71: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 71: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 71: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 71: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 71: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 71: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 71: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 71: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 71: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 71: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 71: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 71: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 71: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 71: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 71: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 71: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 71: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 71: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 71: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 71: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 71: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 71: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 71: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 71: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 71: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 71: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 71: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 71: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 71: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 71: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 71: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 71: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 71: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 71: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 71: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 71: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 71: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 71: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 71: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 71: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 71: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 71: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 71: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 71: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 71: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 71: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 71: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 71: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 71: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 71: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 71: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 71: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 71: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 71: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 71: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 71: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 71: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 71: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 71: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 71: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 71: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 71: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 71: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 71: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 71: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 71: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 71: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 71: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 71: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 71: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 71: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 71: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 71: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 71: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 71: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 71: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 71: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 71: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 71: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 71: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 71: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 71: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 71: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 71: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 71: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 71: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 71: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 71: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 71: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 71: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 71: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 71: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 71: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 71: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 71: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 71: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 71: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 71: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 71: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 71: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 71: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 71: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 71: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 71: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 71: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 71: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 71: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 71: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 71: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 71: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 71: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 71: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 71: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 71: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 71: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 71: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 71: atom (156): 71: atom[0]={name="N"} 71: atom[1]={name="H1"} 71: atom[2]={name="H2"} 71: atom[3]={name="H3"} 71: atom[4]={name="CA"} 71: atom[5]={name="HA"} 71: atom[6]={name="CB"} 71: atom[7]={name="HB1"} 71: atom[8]={name="HB2"} 71: atom[9]={name="CG"} 71: atom[10]={name="HG1"} 71: atom[11]={name="HG2"} 71: atom[12]={name="CD"} 71: atom[13]={name="HD1"} 71: atom[14]={name="HD2"} 71: atom[15]={name="CE"} 71: atom[16]={name="HE1"} 71: atom[17]={name="HE2"} 71: atom[18]={name="NZ"} 71: atom[19]={name="HZ1"} 71: atom[20]={name="HZ2"} 71: atom[21]={name="HZ3"} 71: atom[22]={name="C"} 71: atom[23]={name="O"} 71: atom[24]={name="N"} 71: atom[25]={name="H"} 71: atom[26]={name="CA"} 71: atom[27]={name="HA"} 71: atom[28]={name="CB"} 71: atom[29]={name="HB"} 71: atom[30]={name="CG1"} 71: atom[31]={name="HG11"} 71: atom[32]={name="HG12"} 71: atom[33]={name="HG13"} 71: atom[34]={name="CG2"} 71: atom[35]={name="HG21"} 71: atom[36]={name="HG22"} 71: atom[37]={name="HG23"} 71: atom[38]={name="C"} 71: atom[39]={name="O"} 71: atom[40]={name="N"} 71: atom[41]={name="H"} 71: atom[42]={name="CA"} 71: atom[43]={name="HA"} 71: atom[44]={name="CB"} 71: atom[45]={name="HB1"} 71: atom[46]={name="HB2"} 71: atom[47]={name="CG"} 71: atom[48]={name="CD1"} 71: atom[49]={name="HD1"} 71: atom[50]={name="CD2"} 71: atom[51]={name="HD2"} 71: atom[52]={name="CE1"} 71: atom[53]={name="HE1"} 71: atom[54]={name="CE2"} 71: atom[55]={name="HE2"} 71: atom[56]={name="CZ"} 71: atom[57]={name="HZ"} 71: atom[58]={name="C"} 71: atom[59]={name="O"} 71: atom[60]={name="N"} 71: atom[61]={name="H"} 71: atom[62]={name="CA"} 71: atom[63]={name="HA1"} 71: atom[64]={name="HA2"} 71: atom[65]={name="C"} 71: atom[66]={name="O"} 71: atom[67]={name="N"} 71: atom[68]={name="H"} 71: atom[69]={name="CA"} 71: atom[70]={name="HA"} 71: atom[71]={name="CB"} 71: atom[72]={name="HB1"} 71: atom[73]={name="HB2"} 71: atom[74]={name="CG"} 71: atom[75]={name="HG1"} 71: atom[76]={name="HG2"} 71: atom[77]={name="CD"} 71: atom[78]={name="HD1"} 71: atom[79]={name="HD2"} 71: atom[80]={name="NE"} 71: atom[81]={name="HE"} 71: atom[82]={name="CZ"} 71: atom[83]={name="NH1"} 71: atom[84]={name="HH11"} 71: atom[85]={name="HH12"} 71: atom[86]={name="NH2"} 71: atom[87]={name="HH21"} 71: atom[88]={name="HH22"} 71: atom[89]={name="C"} 71: atom[90]={name="O"} 71: atom[91]={name="N"} 71: atom[92]={name="H"} 71: atom[93]={name="CA"} 71: atom[94]={name="HA"} 71: atom[95]={name="CB"} 71: atom[96]={name="HB1"} 71: atom[97]={name="HB2"} 71: atom[98]={name="SG"} 71: atom[99]={name="HG"} 71: atom[100]={name="C"} 71: atom[101]={name="O"} 71: atom[102]={name="N"} 71: atom[103]={name="H"} 71: atom[104]={name="CA"} 71: atom[105]={name="HA"} 71: atom[106]={name="CB"} 71: atom[107]={name="HB1"} 71: atom[108]={name="HB2"} 71: atom[109]={name="CG"} 71: atom[110]={name="HG1"} 71: atom[111]={name="HG2"} 71: atom[112]={name="CD"} 71: atom[113]={name="OE1"} 71: atom[114]={name="OE2"} 71: atom[115]={name="C"} 71: atom[116]={name="O"} 71: atom[117]={name="N"} 71: atom[118]={name="H"} 71: atom[119]={name="CA"} 71: atom[120]={name="HA"} 71: atom[121]={name="CB"} 71: atom[122]={name="HB1"} 71: atom[123]={name="HB2"} 71: atom[124]={name="CG"} 71: atom[125]={name="HG"} 71: atom[126]={name="CD1"} 71: atom[127]={name="HD11"} 71: atom[128]={name="HD12"} 71: atom[129]={name="HD13"} 71: atom[130]={name="CD2"} 71: atom[131]={name="HD21"} 71: atom[132]={name="HD22"} 71: atom[133]={name="HD23"} 71: atom[134]={name="C"} 71: atom[135]={name="O"} 71: atom[136]={name="N"} 71: atom[137]={name="H"} 71: atom[138]={name="CA"} 71: atom[139]={name="HA"} 71: atom[140]={name="CB"} 71: atom[141]={name="HB1"} 71: atom[142]={name="HB2"} 71: atom[143]={name="HB3"} 71: atom[144]={name="C"} 71: atom[145]={name="O"} 71: atom[146]={name="N"} 71: atom[147]={name="H"} 71: atom[148]={name="CA"} 71: atom[149]={name="HA"} 71: atom[150]={name="CB"} 71: atom[151]={name="HB1"} 71: atom[152]={name="HB2"} 71: atom[153]={name="HB3"} 71: atom[154]={name="C"} 71: atom[155]={name="O"} 71: type (156): 71: type[0]={name="opls_287",nameB="opls_287"} 71: type[1]={name="opls_290",nameB="opls_290"} 71: type[2]={name="opls_290",nameB="opls_290"} 71: type[3]={name="opls_290",nameB="opls_290"} 71: type[4]={name="opls_293B",nameB="opls_293B"} 71: type[5]={name="opls_140",nameB="opls_140"} 71: type[6]={name="opls_136",nameB="opls_136"} 71: type[7]={name="opls_140",nameB="opls_140"} 71: type[8]={name="opls_140",nameB="opls_140"} 71: type[9]={name="opls_136",nameB="opls_136"} 71: type[10]={name="opls_140",nameB="opls_140"} 71: type[11]={name="opls_140",nameB="opls_140"} 71: type[12]={name="opls_136",nameB="opls_136"} 71: type[13]={name="opls_140",nameB="opls_140"} 71: type[14]={name="opls_140",nameB="opls_140"} 71: type[15]={name="opls_292",nameB="opls_292"} 71: type[16]={name="opls_140",nameB="opls_140"} 71: type[17]={name="opls_140",nameB="opls_140"} 71: type[18]={name="opls_287",nameB="opls_287"} 71: type[19]={name="opls_290",nameB="opls_290"} 71: type[20]={name="opls_290",nameB="opls_290"} 71: type[21]={name="opls_290",nameB="opls_290"} 71: type[22]={name="opls_235",nameB="opls_235"} 71: type[23]={name="opls_236",nameB="opls_236"} 71: type[24]={name="opls_238",nameB="opls_238"} 71: type[25]={name="opls_241",nameB="opls_241"} 71: type[26]={name="opls_224B",nameB="opls_224B"} 71: type[27]={name="opls_140",nameB="opls_140"} 71: type[28]={name="opls_137",nameB="opls_137"} 71: type[29]={name="opls_140",nameB="opls_140"} 71: type[30]={name="opls_135",nameB="opls_135"} 71: type[31]={name="opls_140",nameB="opls_140"} 71: type[32]={name="opls_140",nameB="opls_140"} 71: type[33]={name="opls_140",nameB="opls_140"} 71: type[34]={name="opls_135",nameB="opls_135"} 71: type[35]={name="opls_140",nameB="opls_140"} 71: type[36]={name="opls_140",nameB="opls_140"} 71: type[37]={name="opls_140",nameB="opls_140"} 71: type[38]={name="opls_235",nameB="opls_235"} 71: type[39]={name="opls_236",nameB="opls_236"} 71: type[40]={name="opls_238",nameB="opls_238"} 71: type[41]={name="opls_241",nameB="opls_241"} 71: type[42]={name="opls_224B",nameB="opls_224B"} 71: type[43]={name="opls_140",nameB="opls_140"} 71: type[44]={name="opls_149",nameB="opls_149"} 71: type[45]={name="opls_140",nameB="opls_140"} 71: type[46]={name="opls_140",nameB="opls_140"} 71: type[47]={name="opls_145",nameB="opls_145"} 71: type[48]={name="opls_145",nameB="opls_145"} 71: type[49]={name="opls_146",nameB="opls_146"} 71: type[50]={name="opls_145",nameB="opls_145"} 71: type[51]={name="opls_146",nameB="opls_146"} 71: type[52]={name="opls_145",nameB="opls_145"} 71: type[53]={name="opls_146",nameB="opls_146"} 71: type[54]={name="opls_145",nameB="opls_145"} 71: type[55]={name="opls_146",nameB="opls_146"} 71: type[56]={name="opls_145",nameB="opls_145"} 71: type[57]={name="opls_146",nameB="opls_146"} 71: type[58]={name="opls_235",nameB="opls_235"} 71: type[59]={name="opls_236",nameB="opls_236"} 71: type[60]={name="opls_238",nameB="opls_238"} 71: type[61]={name="opls_241",nameB="opls_241"} 71: type[62]={name="opls_223B",nameB="opls_223B"} 71: type[63]={name="opls_140",nameB="opls_140"} 71: type[64]={name="opls_140",nameB="opls_140"} 71: type[65]={name="opls_235",nameB="opls_235"} 71: type[66]={name="opls_236",nameB="opls_236"} 71: type[67]={name="opls_238",nameB="opls_238"} 71: type[68]={name="opls_241",nameB="opls_241"} 71: type[69]={name="opls_224B",nameB="opls_224B"} 71: type[70]={name="opls_140",nameB="opls_140"} 71: type[71]={name="opls_136",nameB="opls_136"} 71: type[72]={name="opls_140",nameB="opls_140"} 71: type[73]={name="opls_140",nameB="opls_140"} 71: type[74]={name="opls_308",nameB="opls_308"} 71: type[75]={name="opls_140",nameB="opls_140"} 71: type[76]={name="opls_140",nameB="opls_140"} 71: type[77]={name="opls_307",nameB="opls_307"} 71: type[78]={name="opls_140",nameB="opls_140"} 71: type[79]={name="opls_140",nameB="opls_140"} 71: type[80]={name="opls_303",nameB="opls_303"} 71: type[81]={name="opls_304",nameB="opls_304"} 71: type[82]={name="opls_302",nameB="opls_302"} 71: type[83]={name="opls_300",nameB="opls_300"} 71: type[84]={name="opls_301",nameB="opls_301"} 71: type[85]={name="opls_301",nameB="opls_301"} 71: type[86]={name="opls_300",nameB="opls_300"} 71: type[87]={name="opls_301",nameB="opls_301"} 71: type[88]={name="opls_301",nameB="opls_301"} 71: type[89]={name="opls_235",nameB="opls_235"} 71: type[90]={name="opls_236",nameB="opls_236"} 71: type[91]={name="opls_238",nameB="opls_238"} 71: type[92]={name="opls_241",nameB="opls_241"} 71: type[93]={name="opls_224B",nameB="opls_224B"} 71: type[94]={name="opls_140",nameB="opls_140"} 71: type[95]={name="opls_206",nameB="opls_206"} 71: type[96]={name="opls_140",nameB="opls_140"} 71: type[97]={name="opls_140",nameB="opls_140"} 71: type[98]={name="opls_200",nameB="opls_200"} 71: type[99]={name="opls_204",nameB="opls_204"} 71: type[100]={name="opls_235",nameB="opls_235"} 71: type[101]={name="opls_236",nameB="opls_236"} 71: type[102]={name="opls_238",nameB="opls_238"} 71: type[103]={name="opls_241",nameB="opls_241"} 71: type[104]={name="opls_224B",nameB="opls_224B"} 71: type[105]={name="opls_140",nameB="opls_140"} 71: type[106]={name="opls_136",nameB="opls_136"} 71: type[107]={name="opls_140",nameB="opls_140"} 71: type[108]={name="opls_140",nameB="opls_140"} 71: type[109]={name="opls_274",nameB="opls_274"} 71: type[110]={name="opls_140",nameB="opls_140"} 71: type[111]={name="opls_140",nameB="opls_140"} 71: type[112]={name="opls_271",nameB="opls_271"} 71: type[113]={name="opls_272",nameB="opls_272"} 71: type[114]={name="opls_272",nameB="opls_272"} 71: type[115]={name="opls_235",nameB="opls_235"} 71: type[116]={name="opls_236",nameB="opls_236"} 71: type[117]={name="opls_238",nameB="opls_238"} 71: type[118]={name="opls_241",nameB="opls_241"} 71: type[119]={name="opls_224B",nameB="opls_224B"} 71: type[120]={name="opls_140",nameB="opls_140"} 71: type[121]={name="opls_136",nameB="opls_136"} 71: type[122]={name="opls_140",nameB="opls_140"} 71: type[123]={name="opls_140",nameB="opls_140"} 71: type[124]={name="opls_137",nameB="opls_137"} 71: type[125]={name="opls_140",nameB="opls_140"} 71: type[126]={name="opls_135",nameB="opls_135"} 71: type[127]={name="opls_140",nameB="opls_140"} 71: type[128]={name="opls_140",nameB="opls_140"} 71: type[129]={name="opls_140",nameB="opls_140"} 71: type[130]={name="opls_135",nameB="opls_135"} 71: type[131]={name="opls_140",nameB="opls_140"} 71: type[132]={name="opls_140",nameB="opls_140"} 71: type[133]={name="opls_140",nameB="opls_140"} 71: type[134]={name="opls_235",nameB="opls_235"} 71: type[135]={name="opls_236",nameB="opls_236"} 71: type[136]={name="opls_238",nameB="opls_238"} 71: type[137]={name="opls_241",nameB="opls_241"} 71: type[138]={name="opls_224B",nameB="opls_224B"} 71: type[139]={name="opls_140",nameB="opls_140"} 71: type[140]={name="opls_135",nameB="opls_135"} 71: type[141]={name="opls_140",nameB="opls_140"} 71: type[142]={name="opls_140",nameB="opls_140"} 71: type[143]={name="opls_140",nameB="opls_140"} 71: type[144]={name="opls_235",nameB="opls_235"} 71: type[145]={name="opls_236",nameB="opls_236"} 71: type[146]={name="opls_238",nameB="opls_238"} 71: type[147]={name="opls_241",nameB="opls_241"} 71: type[148]={name="opls_224B",nameB="opls_224B"} 71: type[149]={name="opls_140",nameB="opls_140"} 71: type[150]={name="opls_135",nameB="opls_135"} 71: type[151]={name="opls_140",nameB="opls_140"} 71: type[152]={name="opls_140",nameB="opls_140"} 71: type[153]={name="opls_140",nameB="opls_140"} 71: type[154]={name="opls_235",nameB="opls_235"} 71: type[155]={name="opls_236",nameB="opls_236"} 71: residue (10): 71: residue[0]={name="LYS", nr=1, ic=' '} 71: residue[1]={name="VAL", nr=2, ic=' '} 71: residue[2]={name="PHE", nr=3, ic=' '} 71: residue[3]={name="GLY", nr=4, ic=' '} 71: residue[4]={name="ARG", nr=5, ic=' '} 71: residue[5]={name="CYS", nr=6, ic=' '} 71: residue[6]={name="GLU", nr=7, ic=' '} 71: residue[7]={name="LEU", nr=8, ic=' '} 71: residue[8]={name="ALA", nr=9, ic=' '} 71: residue[9]={name="ALA", nr=10, ic=' '} 71: excls: 71: numLists=156 71: numElements=1828 71: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 71: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 71: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 71: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 71: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 71: 23, 24, 25, 26} 71: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 71: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 71: 14, 15, 22, 23, 24} 71: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 71: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 71: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 71: 16, 17, 18, 22} 71: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 71: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 71: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 71: 17, 18, 19, 20, 21} 71: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 71: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 71: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 71: 20, 21} 71: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 71: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 71: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 71: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 71: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 71: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 71: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 71: 26, 27, 28, 38} 71: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 71: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 71: 30, 34, 38, 39, 40} 71: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 71: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 71: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 71: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 71: 40} 71: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 71: 34, 35, 36, 37, 38, 39, 40} 71: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 71: 36, 37, 38} 71: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 71: 36, 37, 38} 71: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 71: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 71: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 71: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 71: 36, 37, 38} 71: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 71: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 71: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 71: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 71: 40, 41, 42, 43, 44, 58} 71: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 71: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 71: 45, 46, 47, 58, 59, 60} 71: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 71: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 71: 48, 50, 58, 59, 60, 61, 62} 71: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 71: 60} 71: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 71: 50, 51, 52, 54, 58, 59, 60} 71: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 71: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 71: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 71: 52, 53, 54, 55, 56, 58} 71: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 71: 54, 56, 57} 71: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 71: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 71: 55, 56, 57} 71: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 71: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 71: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 71: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 71: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 71: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 71: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 71: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 71: 60, 61, 62, 63, 64, 65} 71: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 71: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 71: 65, 66, 67} 71: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 71: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 71: 68, 69} 71: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 71: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 71: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 71: 70, 71, 89} 71: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 71: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 71: 72, 73, 74, 89, 90, 91} 71: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 71: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 71: 75, 76, 77, 89, 90, 91, 92, 93} 71: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 71: 91} 71: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 71: 77, 78, 79, 80, 89, 90, 91} 71: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 71: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 71: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 71: 79, 80, 81, 82, 89} 71: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 71: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 71: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 71: 81, 82, 83, 86} 71: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 71: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 71: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 71: 84, 85, 86, 87, 88} 71: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 71: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 71: 87, 88} 71: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 71: excls[84][num=6]={80, 82, 83, 84, 85, 86} 71: excls[85][num=6]={80, 82, 83, 84, 85, 86} 71: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 71: excls[87][num=6]={80, 82, 83, 86, 87, 88} 71: excls[88][num=6]={80, 82, 83, 86, 87, 88} 71: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 71: 91, 92, 93, 94, 95, 100} 71: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 71: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 71: 96, 97, 98, 100, 101, 102} 71: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 71: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 71: 99, 100, 101, 102, 103, 104} 71: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 71: 102} 71: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 71: 101, 102} 71: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 71: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 71: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 71: excls[99][num=6]={93, 95, 96, 97, 98, 99} 71: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 71: 102, 103, 104, 105, 106, 115} 71: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 71: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 71: 106, 107, 108, 109, 115, 116, 117} 71: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 71: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 71: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 71: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 71: 115, 116, 117} 71: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 71: 110, 111, 112, 113, 114, 115, 116, 117} 71: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 71: 112, 115} 71: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 71: 112, 115} 71: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 71: 112, 113, 114, 115} 71: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 71: 114} 71: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 71: 114} 71: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 71: 114} 71: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 71: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 71: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 71: 115, 116, 117, 118, 119, 120, 121, 134} 71: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 71: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 71: 120, 121, 122, 123, 124, 134, 135, 136} 71: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 71: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 71: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 71: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 71: 134, 135, 136} 71: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 71: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 71: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 71: 130, 134} 71: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 71: 130, 134} 71: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 71: 127, 128, 129, 130, 131, 132, 133, 134} 71: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 71: 129, 130, 131, 132, 133} 71: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 71: 129, 130, 131, 132, 133} 71: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 71: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 71: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 71: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 71: 129, 130, 131, 132, 133} 71: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 71: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 71: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 71: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 71: 134, 135, 136, 137, 138, 139, 140, 144} 71: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 71: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 71: 139, 140, 141, 142, 143, 144, 145, 146} 71: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 71: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 71: 142, 143, 144, 145, 146, 147, 148} 71: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 71: 144, 145, 146} 71: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 71: 144, 145, 146} 71: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 71: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 71: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 71: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 71: 144, 145, 146, 147, 148, 149, 150, 154} 71: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 71: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 71: 149, 150, 151, 152, 153, 154, 155} 71: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 71: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 71: 152, 153, 154, 155} 71: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 71: 154, 155} 71: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 71: 154, 155} 71: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 71: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 71: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 71: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 71: 154, 155} 71: excls[155][num=6]={146, 148, 149, 150, 154, 155} 71: Bond: 71: nr: 468 71: iatoms: 71: 0 type=100 (BONDS) 0 1 71: 1 type=100 (BONDS) 0 2 71: 2 type=100 (BONDS) 0 3 71: 3 type=101 (BONDS) 0 4 71: 4 type=102 (BONDS) 4 5 71: 5 type=103 (BONDS) 4 6 71: 6 type=104 (BONDS) 4 22 71: 7 type=102 (BONDS) 6 7 71: 8 type=102 (BONDS) 6 8 71: 9 type=103 (BONDS) 6 9 71: 10 type=102 (BONDS) 9 10 71: 11 type=102 (BONDS) 9 11 71: 12 type=103 (BONDS) 9 12 71: 13 type=102 (BONDS) 12 13 71: 14 type=102 (BONDS) 12 14 71: 15 type=103 (BONDS) 12 15 71: 16 type=102 (BONDS) 15 16 71: 17 type=102 (BONDS) 15 17 71: 18 type=101 (BONDS) 15 18 71: 19 type=100 (BONDS) 18 19 71: 20 type=100 (BONDS) 18 20 71: 21 type=100 (BONDS) 18 21 71: 22 type=105 (BONDS) 22 23 71: 23 type=106 (BONDS) 22 24 71: 24 type=100 (BONDS) 24 25 71: 25 type=107 (BONDS) 24 26 71: 26 type=102 (BONDS) 26 27 71: 27 type=103 (BONDS) 26 28 71: 28 type=104 (BONDS) 26 38 71: 29 type=102 (BONDS) 28 29 71: 30 type=103 (BONDS) 28 30 71: 31 type=103 (BONDS) 28 34 71: 32 type=102 (BONDS) 30 31 71: 33 type=102 (BONDS) 30 32 71: 34 type=102 (BONDS) 30 33 71: 35 type=102 (BONDS) 34 35 71: 36 type=102 (BONDS) 34 36 71: 37 type=102 (BONDS) 34 37 71: 38 type=105 (BONDS) 38 39 71: 39 type=106 (BONDS) 38 40 71: 40 type=100 (BONDS) 40 41 71: 41 type=107 (BONDS) 40 42 71: 42 type=102 (BONDS) 42 43 71: 43 type=103 (BONDS) 42 44 71: 44 type=104 (BONDS) 42 58 71: 45 type=102 (BONDS) 44 45 71: 46 type=102 (BONDS) 44 46 71: 47 type=108 (BONDS) 44 47 71: 48 type=109 (BONDS) 47 48 71: 49 type=109 (BONDS) 47 50 71: 50 type=110 (BONDS) 48 49 71: 51 type=109 (BONDS) 48 52 71: 52 type=110 (BONDS) 50 51 71: 53 type=109 (BONDS) 50 54 71: 54 type=110 (BONDS) 52 53 71: 55 type=109 (BONDS) 52 56 71: 56 type=110 (BONDS) 54 55 71: 57 type=109 (BONDS) 54 56 71: 58 type=110 (BONDS) 56 57 71: 59 type=105 (BONDS) 58 59 71: 60 type=106 (BONDS) 58 60 71: 61 type=100 (BONDS) 60 61 71: 62 type=107 (BONDS) 60 62 71: 63 type=102 (BONDS) 62 63 71: 64 type=102 (BONDS) 62 64 71: 65 type=104 (BONDS) 62 65 71: 66 type=105 (BONDS) 65 66 71: 67 type=106 (BONDS) 65 67 71: 68 type=100 (BONDS) 67 68 71: 69 type=107 (BONDS) 67 69 71: 70 type=102 (BONDS) 69 70 71: 71 type=103 (BONDS) 69 71 71: 72 type=104 (BONDS) 69 89 71: 73 type=102 (BONDS) 71 72 71: 74 type=102 (BONDS) 71 73 71: 75 type=103 (BONDS) 71 74 71: 76 type=102 (BONDS) 74 75 71: 77 type=102 (BONDS) 74 76 71: 78 type=103 (BONDS) 74 77 71: 79 type=102 (BONDS) 77 78 71: 80 type=102 (BONDS) 77 79 71: 81 type=111 (BONDS) 77 80 71: 82 type=100 (BONDS) 80 81 71: 83 type=112 (BONDS) 80 82 71: 84 type=112 (BONDS) 82 83 71: 85 type=112 (BONDS) 82 86 71: 86 type=100 (BONDS) 83 84 71: 87 type=100 (BONDS) 83 85 71: 88 type=100 (BONDS) 86 87 71: 89 type=100 (BONDS) 86 88 71: 90 type=105 (BONDS) 89 90 71: 91 type=106 (BONDS) 89 91 71: 92 type=100 (BONDS) 91 92 71: 93 type=107 (BONDS) 91 93 71: 94 type=102 (BONDS) 93 94 71: 95 type=103 (BONDS) 93 95 71: 96 type=104 (BONDS) 93 100 71: 97 type=102 (BONDS) 95 96 71: 98 type=102 (BONDS) 95 97 71: 99 type=113 (BONDS) 95 98 71: 100 type=114 (BONDS) 98 99 71: 101 type=105 (BONDS) 100 101 71: 102 type=106 (BONDS) 100 102 71: 103 type=100 (BONDS) 102 103 71: 104 type=107 (BONDS) 102 104 71: 105 type=102 (BONDS) 104 105 71: 106 type=103 (BONDS) 104 106 71: 107 type=104 (BONDS) 104 115 71: 108 type=102 (BONDS) 106 107 71: 109 type=102 (BONDS) 106 108 71: 110 type=103 (BONDS) 106 109 71: 111 type=102 (BONDS) 109 110 71: 112 type=102 (BONDS) 109 111 71: 113 type=104 (BONDS) 109 112 71: 114 type=115 (BONDS) 112 113 71: 115 type=115 (BONDS) 112 114 71: 116 type=105 (BONDS) 115 116 71: 117 type=106 (BONDS) 115 117 71: 118 type=100 (BONDS) 117 118 71: 119 type=107 (BONDS) 117 119 71: 120 type=102 (BONDS) 119 120 71: 121 type=103 (BONDS) 119 121 71: 122 type=104 (BONDS) 119 134 71: 123 type=102 (BONDS) 121 122 71: 124 type=102 (BONDS) 121 123 71: 125 type=103 (BONDS) 121 124 71: 126 type=102 (BONDS) 124 125 71: 127 type=103 (BONDS) 124 126 71: 128 type=103 (BONDS) 124 130 71: 129 type=102 (BONDS) 126 127 71: 130 type=102 (BONDS) 126 128 71: 131 type=102 (BONDS) 126 129 71: 132 type=102 (BONDS) 130 131 71: 133 type=102 (BONDS) 130 132 71: 134 type=102 (BONDS) 130 133 71: 135 type=105 (BONDS) 134 135 71: 136 type=106 (BONDS) 134 136 71: 137 type=100 (BONDS) 136 137 71: 138 type=107 (BONDS) 136 138 71: 139 type=102 (BONDS) 138 139 71: 140 type=103 (BONDS) 138 140 71: 141 type=104 (BONDS) 138 144 71: 142 type=102 (BONDS) 140 141 71: 143 type=102 (BONDS) 140 142 71: 144 type=102 (BONDS) 140 143 71: 145 type=105 (BONDS) 144 145 71: 146 type=106 (BONDS) 144 146 71: 147 type=100 (BONDS) 146 147 71: 148 type=107 (BONDS) 146 148 71: 149 type=102 (BONDS) 148 149 71: 150 type=103 (BONDS) 148 150 71: 151 type=104 (BONDS) 148 154 71: 152 type=102 (BONDS) 150 151 71: 153 type=102 (BONDS) 150 152 71: 154 type=102 (BONDS) 150 153 71: 155 type=105 (BONDS) 154 155 71: G96Bond: 71: nr: 0 71: Morse: 71: nr: 0 71: Cubic Bonds: 71: nr: 0 71: Connect Bonds: 71: nr: 0 71: Harmonic Pot.: 71: nr: 0 71: FENE Bonds: 71: nr: 0 71: Tab. Bonds: 71: nr: 0 71: Tab. Bonds NC: 71: nr: 0 71: Restraint Pot.: 71: nr: 0 71: Angle: 71: nr: 1124 71: iatoms: 71: 0 type=116 (ANGLES) 1 0 2 71: 1 type=116 (ANGLES) 1 0 3 71: 2 type=116 (ANGLES) 1 0 4 71: 3 type=116 (ANGLES) 2 0 3 71: 4 type=116 (ANGLES) 2 0 4 71: 5 type=116 (ANGLES) 3 0 4 71: 6 type=116 (ANGLES) 0 4 5 71: 7 type=117 (ANGLES) 0 4 6 71: 8 type=117 (ANGLES) 0 4 22 71: 9 type=118 (ANGLES) 5 4 6 71: 10 type=116 (ANGLES) 5 4 22 71: 11 type=119 (ANGLES) 6 4 22 71: 12 type=118 (ANGLES) 4 6 7 71: 13 type=118 (ANGLES) 4 6 8 71: 14 type=120 (ANGLES) 4 6 9 71: 15 type=121 (ANGLES) 7 6 8 71: 16 type=118 (ANGLES) 7 6 9 71: 17 type=118 (ANGLES) 8 6 9 71: 18 type=118 (ANGLES) 6 9 10 71: 19 type=118 (ANGLES) 6 9 11 71: 20 type=120 (ANGLES) 6 9 12 71: 21 type=121 (ANGLES) 10 9 11 71: 22 type=118 (ANGLES) 10 9 12 71: 23 type=118 (ANGLES) 11 9 12 71: 24 type=118 (ANGLES) 9 12 13 71: 25 type=118 (ANGLES) 9 12 14 71: 26 type=120 (ANGLES) 9 12 15 71: 27 type=121 (ANGLES) 13 12 14 71: 28 type=118 (ANGLES) 13 12 15 71: 29 type=118 (ANGLES) 14 12 15 71: 30 type=118 (ANGLES) 12 15 16 71: 31 type=118 (ANGLES) 12 15 17 71: 32 type=117 (ANGLES) 12 15 18 71: 33 type=121 (ANGLES) 16 15 17 71: 34 type=116 (ANGLES) 16 15 18 71: 35 type=116 (ANGLES) 17 15 18 71: 36 type=116 (ANGLES) 15 18 19 71: 37 type=116 (ANGLES) 15 18 20 71: 38 type=116 (ANGLES) 15 18 21 71: 39 type=116 (ANGLES) 19 18 20 71: 40 type=116 (ANGLES) 19 18 21 71: 41 type=116 (ANGLES) 20 18 21 71: 42 type=122 (ANGLES) 4 22 23 71: 43 type=123 (ANGLES) 4 22 24 71: 44 type=124 (ANGLES) 23 22 24 71: 45 type=125 (ANGLES) 22 24 25 71: 46 type=126 (ANGLES) 22 24 26 71: 47 type=127 (ANGLES) 25 24 26 71: 48 type=116 (ANGLES) 24 26 27 71: 49 type=128 (ANGLES) 24 26 28 71: 50 type=129 (ANGLES) 24 26 38 71: 51 type=118 (ANGLES) 27 26 28 71: 52 type=116 (ANGLES) 27 26 38 71: 53 type=119 (ANGLES) 28 26 38 71: 54 type=118 (ANGLES) 26 28 29 71: 55 type=120 (ANGLES) 26 28 30 71: 56 type=120 (ANGLES) 26 28 34 71: 57 type=118 (ANGLES) 29 28 30 71: 58 type=118 (ANGLES) 29 28 34 71: 59 type=120 (ANGLES) 30 28 34 71: 60 type=118 (ANGLES) 28 30 31 71: 61 type=118 (ANGLES) 28 30 32 71: 62 type=118 (ANGLES) 28 30 33 71: 63 type=121 (ANGLES) 31 30 32 71: 64 type=121 (ANGLES) 31 30 33 71: 65 type=121 (ANGLES) 32 30 33 71: 66 type=118 (ANGLES) 28 34 35 71: 67 type=118 (ANGLES) 28 34 36 71: 68 type=118 (ANGLES) 28 34 37 71: 69 type=121 (ANGLES) 35 34 36 71: 70 type=121 (ANGLES) 35 34 37 71: 71 type=121 (ANGLES) 36 34 37 71: 72 type=122 (ANGLES) 26 38 39 71: 73 type=123 (ANGLES) 26 38 40 71: 74 type=124 (ANGLES) 39 38 40 71: 75 type=125 (ANGLES) 38 40 41 71: 76 type=126 (ANGLES) 38 40 42 71: 77 type=127 (ANGLES) 41 40 42 71: 78 type=116 (ANGLES) 40 42 43 71: 79 type=128 (ANGLES) 40 42 44 71: 80 type=129 (ANGLES) 40 42 58 71: 81 type=118 (ANGLES) 43 42 44 71: 82 type=116 (ANGLES) 43 42 58 71: 83 type=119 (ANGLES) 44 42 58 71: 84 type=118 (ANGLES) 42 44 45 71: 85 type=118 (ANGLES) 42 44 46 71: 86 type=130 (ANGLES) 42 44 47 71: 87 type=121 (ANGLES) 45 44 46 71: 88 type=116 (ANGLES) 45 44 47 71: 89 type=116 (ANGLES) 46 44 47 71: 90 type=131 (ANGLES) 44 47 48 71: 91 type=131 (ANGLES) 44 47 50 71: 92 type=132 (ANGLES) 48 47 50 71: 93 type=133 (ANGLES) 47 48 49 71: 94 type=132 (ANGLES) 47 48 52 71: 95 type=133 (ANGLES) 49 48 52 71: 96 type=133 (ANGLES) 47 50 51 71: 97 type=132 (ANGLES) 47 50 54 71: 98 type=133 (ANGLES) 51 50 54 71: 99 type=133 (ANGLES) 48 52 53 71: 100 type=132 (ANGLES) 48 52 56 71: 101 type=133 (ANGLES) 53 52 56 71: 102 type=133 (ANGLES) 50 54 55 71: 103 type=132 (ANGLES) 50 54 56 71: 104 type=133 (ANGLES) 55 54 56 71: 105 type=132 (ANGLES) 52 56 54 71: 106 type=133 (ANGLES) 52 56 57 71: 107 type=133 (ANGLES) 54 56 57 71: 108 type=122 (ANGLES) 42 58 59 71: 109 type=123 (ANGLES) 42 58 60 71: 110 type=124 (ANGLES) 59 58 60 71: 111 type=125 (ANGLES) 58 60 61 71: 112 type=126 (ANGLES) 58 60 62 71: 113 type=127 (ANGLES) 61 60 62 71: 114 type=116 (ANGLES) 60 62 63 71: 115 type=116 (ANGLES) 60 62 64 71: 116 type=129 (ANGLES) 60 62 65 71: 117 type=121 (ANGLES) 63 62 64 71: 118 type=116 (ANGLES) 63 62 65 71: 119 type=116 (ANGLES) 64 62 65 71: 120 type=122 (ANGLES) 62 65 66 71: 121 type=123 (ANGLES) 62 65 67 71: 122 type=124 (ANGLES) 66 65 67 71: 123 type=125 (ANGLES) 65 67 68 71: 124 type=126 (ANGLES) 65 67 69 71: 125 type=127 (ANGLES) 68 67 69 71: 126 type=116 (ANGLES) 67 69 70 71: 127 type=128 (ANGLES) 67 69 71 71: 128 type=129 (ANGLES) 67 69 89 71: 129 type=118 (ANGLES) 70 69 71 71: 130 type=116 (ANGLES) 70 69 89 71: 131 type=119 (ANGLES) 71 69 89 71: 132 type=118 (ANGLES) 69 71 72 71: 133 type=118 (ANGLES) 69 71 73 71: 134 type=120 (ANGLES) 69 71 74 71: 135 type=121 (ANGLES) 72 71 73 71: 136 type=118 (ANGLES) 72 71 74 71: 137 type=118 (ANGLES) 73 71 74 71: 138 type=118 (ANGLES) 71 74 75 71: 139 type=118 (ANGLES) 71 74 76 71: 140 type=120 (ANGLES) 71 74 77 71: 141 type=121 (ANGLES) 75 74 76 71: 142 type=118 (ANGLES) 75 74 77 71: 143 type=118 (ANGLES) 76 74 77 71: 144 type=118 (ANGLES) 74 77 78 71: 145 type=118 (ANGLES) 74 77 79 71: 146 type=117 (ANGLES) 74 77 80 71: 147 type=121 (ANGLES) 78 77 79 71: 148 type=116 (ANGLES) 78 77 80 71: 149 type=116 (ANGLES) 79 77 80 71: 150 type=134 (ANGLES) 77 80 81 71: 151 type=135 (ANGLES) 77 80 82 71: 152 type=133 (ANGLES) 81 80 82 71: 153 type=131 (ANGLES) 80 82 83 71: 154 type=131 (ANGLES) 80 82 86 71: 155 type=131 (ANGLES) 83 82 86 71: 156 type=133 (ANGLES) 82 83 84 71: 157 type=133 (ANGLES) 82 83 85 71: 158 type=133 (ANGLES) 84 83 85 71: 159 type=133 (ANGLES) 82 86 87 71: 160 type=133 (ANGLES) 82 86 88 71: 161 type=133 (ANGLES) 87 86 88 71: 162 type=122 (ANGLES) 69 89 90 71: 163 type=123 (ANGLES) 69 89 91 71: 164 type=124 (ANGLES) 90 89 91 71: 165 type=125 (ANGLES) 89 91 92 71: 166 type=126 (ANGLES) 89 91 93 71: 167 type=127 (ANGLES) 92 91 93 71: 168 type=116 (ANGLES) 91 93 94 71: 169 type=128 (ANGLES) 91 93 95 71: 170 type=129 (ANGLES) 91 93 100 71: 171 type=118 (ANGLES) 94 93 95 71: 172 type=116 (ANGLES) 94 93 100 71: 173 type=119 (ANGLES) 95 93 100 71: 174 type=118 (ANGLES) 93 95 96 71: 175 type=118 (ANGLES) 93 95 97 71: 176 type=136 (ANGLES) 93 95 98 71: 177 type=121 (ANGLES) 96 95 97 71: 178 type=116 (ANGLES) 96 95 98 71: 179 type=116 (ANGLES) 97 95 98 71: 180 type=137 (ANGLES) 95 98 99 71: 181 type=122 (ANGLES) 93 100 101 71: 182 type=123 (ANGLES) 93 100 102 71: 183 type=124 (ANGLES) 101 100 102 71: 184 type=125 (ANGLES) 100 102 103 71: 185 type=126 (ANGLES) 100 102 104 71: 186 type=127 (ANGLES) 103 102 104 71: 187 type=116 (ANGLES) 102 104 105 71: 188 type=128 (ANGLES) 102 104 106 71: 189 type=129 (ANGLES) 102 104 115 71: 190 type=118 (ANGLES) 105 104 106 71: 191 type=116 (ANGLES) 105 104 115 71: 192 type=119 (ANGLES) 106 104 115 71: 193 type=118 (ANGLES) 104 106 107 71: 194 type=118 (ANGLES) 104 106 108 71: 195 type=120 (ANGLES) 104 106 109 71: 196 type=121 (ANGLES) 107 106 108 71: 197 type=118 (ANGLES) 107 106 109 71: 198 type=118 (ANGLES) 108 106 109 71: 199 type=118 (ANGLES) 106 109 110 71: 200 type=118 (ANGLES) 106 109 111 71: 201 type=119 (ANGLES) 106 109 112 71: 202 type=121 (ANGLES) 110 109 111 71: 203 type=116 (ANGLES) 110 109 112 71: 204 type=116 (ANGLES) 111 109 112 71: 205 type=138 (ANGLES) 109 112 113 71: 206 type=138 (ANGLES) 109 112 114 71: 207 type=139 (ANGLES) 113 112 114 71: 208 type=122 (ANGLES) 104 115 116 71: 209 type=123 (ANGLES) 104 115 117 71: 210 type=124 (ANGLES) 116 115 117 71: 211 type=125 (ANGLES) 115 117 118 71: 212 type=126 (ANGLES) 115 117 119 71: 213 type=127 (ANGLES) 118 117 119 71: 214 type=116 (ANGLES) 117 119 120 71: 215 type=128 (ANGLES) 117 119 121 71: 216 type=129 (ANGLES) 117 119 134 71: 217 type=118 (ANGLES) 120 119 121 71: 218 type=116 (ANGLES) 120 119 134 71: 219 type=119 (ANGLES) 121 119 134 71: 220 type=118 (ANGLES) 119 121 122 71: 221 type=118 (ANGLES) 119 121 123 71: 222 type=120 (ANGLES) 119 121 124 71: 223 type=121 (ANGLES) 122 121 123 71: 224 type=118 (ANGLES) 122 121 124 71: 225 type=118 (ANGLES) 123 121 124 71: 226 type=118 (ANGLES) 121 124 125 71: 227 type=120 (ANGLES) 121 124 126 71: 228 type=120 (ANGLES) 121 124 130 71: 229 type=118 (ANGLES) 125 124 126 71: 230 type=118 (ANGLES) 125 124 130 71: 231 type=120 (ANGLES) 126 124 130 71: 232 type=118 (ANGLES) 124 126 127 71: 233 type=118 (ANGLES) 124 126 128 71: 234 type=118 (ANGLES) 124 126 129 71: 235 type=121 (ANGLES) 127 126 128 71: 236 type=121 (ANGLES) 127 126 129 71: 237 type=121 (ANGLES) 128 126 129 71: 238 type=118 (ANGLES) 124 130 131 71: 239 type=118 (ANGLES) 124 130 132 71: 240 type=118 (ANGLES) 124 130 133 71: 241 type=121 (ANGLES) 131 130 132 71: 242 type=121 (ANGLES) 131 130 133 71: 243 type=121 (ANGLES) 132 130 133 71: 244 type=122 (ANGLES) 119 134 135 71: 245 type=123 (ANGLES) 119 134 136 71: 246 type=124 (ANGLES) 135 134 136 71: 247 type=125 (ANGLES) 134 136 137 71: 248 type=126 (ANGLES) 134 136 138 71: 249 type=127 (ANGLES) 137 136 138 71: 250 type=116 (ANGLES) 136 138 139 71: 251 type=128 (ANGLES) 136 138 140 71: 252 type=129 (ANGLES) 136 138 144 71: 253 type=118 (ANGLES) 139 138 140 71: 254 type=116 (ANGLES) 139 138 144 71: 255 type=119 (ANGLES) 140 138 144 71: 256 type=118 (ANGLES) 138 140 141 71: 257 type=118 (ANGLES) 138 140 142 71: 258 type=118 (ANGLES) 138 140 143 71: 259 type=121 (ANGLES) 141 140 142 71: 260 type=121 (ANGLES) 141 140 143 71: 261 type=121 (ANGLES) 142 140 143 71: 262 type=122 (ANGLES) 138 144 145 71: 263 type=123 (ANGLES) 138 144 146 71: 264 type=124 (ANGLES) 145 144 146 71: 265 type=125 (ANGLES) 144 146 147 71: 266 type=126 (ANGLES) 144 146 148 71: 267 type=127 (ANGLES) 147 146 148 71: 268 type=116 (ANGLES) 146 148 149 71: 269 type=128 (ANGLES) 146 148 150 71: 270 type=129 (ANGLES) 146 148 154 71: 271 type=118 (ANGLES) 149 148 150 71: 272 type=116 (ANGLES) 149 148 154 71: 273 type=119 (ANGLES) 150 148 154 71: 274 type=118 (ANGLES) 148 150 151 71: 275 type=118 (ANGLES) 148 150 152 71: 276 type=118 (ANGLES) 148 150 153 71: 277 type=121 (ANGLES) 151 150 152 71: 278 type=121 (ANGLES) 151 150 153 71: 279 type=121 (ANGLES) 152 150 153 71: 280 type=122 (ANGLES) 148 154 155 71: G96Angle: 71: nr: 0 71: Restr. Angles: 71: nr: 0 71: Lin. Angle: 71: nr: 0 71: Bond-Cross: 71: nr: 0 71: BA-Cross: 71: nr: 0 71: U-B: 71: nr: 0 71: Quartic Angles: 71: nr: 0 71: Tab. Angles: 71: nr: 0 71: Proper Dih.: 71: nr: 145 71: iatoms: 71: 0 type=140 (PDIHS) 4 24 22 23 71: 1 type=141 (PDIHS) 22 26 24 25 71: 2 type=140 (PDIHS) 26 40 38 39 71: 3 type=141 (PDIHS) 38 42 40 41 71: 4 type=140 (PDIHS) 42 60 58 59 71: 5 type=142 (PDIHS) 44 47 50 48 71: 6 type=142 (PDIHS) 47 52 48 49 71: 7 type=142 (PDIHS) 47 54 50 51 71: 8 type=142 (PDIHS) 48 56 52 53 71: 9 type=142 (PDIHS) 50 56 54 55 71: 10 type=142 (PDIHS) 52 54 56 57 71: 11 type=141 (PDIHS) 58 62 60 61 71: 12 type=140 (PDIHS) 62 67 65 66 71: 13 type=141 (PDIHS) 65 69 67 68 71: 14 type=140 (PDIHS) 69 91 89 90 71: 15 type=141 (PDIHS) 77 82 80 81 71: 16 type=140 (PDIHS) 80 83 82 86 71: 17 type=141 (PDIHS) 82 84 83 85 71: 18 type=141 (PDIHS) 82 87 86 88 71: 19 type=141 (PDIHS) 89 93 91 92 71: 20 type=140 (PDIHS) 93 102 100 101 71: 21 type=141 (PDIHS) 100 104 102 103 71: 22 type=140 (PDIHS) 104 117 115 116 71: 23 type=140 (PDIHS) 109 113 112 114 71: 24 type=141 (PDIHS) 115 119 117 118 71: 25 type=140 (PDIHS) 119 136 134 135 71: 26 type=141 (PDIHS) 134 138 136 137 71: 27 type=140 (PDIHS) 138 146 144 145 71: 28 type=141 (PDIHS) 144 148 146 147 71: Ryckaert-Bell.: 71: nr: 1565 71: iatoms: 71: 0 type=143 (RBDIHS) 1 0 4 5 71: 1 type=144 (RBDIHS) 1 0 4 6 71: 2 type=144 (RBDIHS) 1 0 4 22 71: 3 type=143 (RBDIHS) 2 0 4 5 71: 4 type=144 (RBDIHS) 2 0 4 6 71: 5 type=144 (RBDIHS) 2 0 4 22 71: 6 type=143 (RBDIHS) 3 0 4 5 71: 7 type=144 (RBDIHS) 3 0 4 6 71: 8 type=144 (RBDIHS) 3 0 4 22 71: 9 type=145 (RBDIHS) 0 4 6 9 71: 10 type=146 (RBDIHS) 22 4 6 9 71: 11 type=147 (RBDIHS) 0 4 6 7 71: 12 type=147 (RBDIHS) 0 4 6 8 71: 13 type=148 (RBDIHS) 5 4 6 7 71: 14 type=148 (RBDIHS) 5 4 6 8 71: 15 type=148 (RBDIHS) 5 4 6 9 71: 16 type=149 (RBDIHS) 22 4 6 7 71: 17 type=149 (RBDIHS) 22 4 6 8 71: 18 type=150 (RBDIHS) 0 4 22 24 71: 19 type=151 (RBDIHS) 6 4 22 24 71: 20 type=148 (RBDIHS) 4 6 9 10 71: 21 type=148 (RBDIHS) 4 6 9 11 71: 22 type=152 (RBDIHS) 4 6 9 12 71: 23 type=148 (RBDIHS) 7 6 9 10 71: 24 type=148 (RBDIHS) 7 6 9 11 71: 25 type=148 (RBDIHS) 7 6 9 12 71: 26 type=148 (RBDIHS) 8 6 9 10 71: 27 type=148 (RBDIHS) 8 6 9 11 71: 28 type=148 (RBDIHS) 8 6 9 12 71: 29 type=148 (RBDIHS) 6 9 12 13 71: 30 type=148 (RBDIHS) 6 9 12 14 71: 31 type=152 (RBDIHS) 6 9 12 15 71: 32 type=148 (RBDIHS) 10 9 12 13 71: 33 type=148 (RBDIHS) 10 9 12 14 71: 34 type=148 (RBDIHS) 10 9 12 15 71: 35 type=148 (RBDIHS) 11 9 12 13 71: 36 type=148 (RBDIHS) 11 9 12 14 71: 37 type=148 (RBDIHS) 11 9 12 15 71: 38 type=148 (RBDIHS) 9 12 15 16 71: 39 type=148 (RBDIHS) 9 12 15 17 71: 40 type=153 (RBDIHS) 9 12 15 18 71: 41 type=148 (RBDIHS) 13 12 15 16 71: 42 type=148 (RBDIHS) 13 12 15 17 71: 43 type=154 (RBDIHS) 13 12 15 18 71: 44 type=148 (RBDIHS) 14 12 15 16 71: 45 type=148 (RBDIHS) 14 12 15 17 71: 46 type=154 (RBDIHS) 14 12 15 18 71: 47 type=144 (RBDIHS) 12 15 18 19 71: 48 type=144 (RBDIHS) 12 15 18 20 71: 49 type=144 (RBDIHS) 12 15 18 21 71: 50 type=143 (RBDIHS) 16 15 18 19 71: 51 type=143 (RBDIHS) 16 15 18 20 71: 52 type=143 (RBDIHS) 16 15 18 21 71: 53 type=143 (RBDIHS) 17 15 18 19 71: 54 type=143 (RBDIHS) 17 15 18 20 71: 55 type=143 (RBDIHS) 17 15 18 21 71: 56 type=155 (RBDIHS) 4 22 24 25 71: 57 type=156 (RBDIHS) 4 22 24 26 71: 58 type=155 (RBDIHS) 23 22 24 25 71: 59 type=157 (RBDIHS) 23 22 24 26 71: 60 type=158 (RBDIHS) 22 24 26 28 71: 61 type=159 (RBDIHS) 22 24 26 38 71: 62 type=160 (RBDIHS) 24 26 28 30 71: 63 type=160 (RBDIHS) 24 26 28 34 71: 64 type=161 (RBDIHS) 38 26 28 30 71: 65 type=161 (RBDIHS) 38 26 28 34 71: 66 type=147 (RBDIHS) 24 26 28 29 71: 67 type=148 (RBDIHS) 27 26 28 29 71: 68 type=148 (RBDIHS) 27 26 28 30 71: 69 type=148 (RBDIHS) 27 26 28 34 71: 70 type=149 (RBDIHS) 38 26 28 29 71: 71 type=150 (RBDIHS) 24 26 38 40 71: 72 type=151 (RBDIHS) 28 26 38 40 71: 73 type=148 (RBDIHS) 26 28 30 31 71: 74 type=148 (RBDIHS) 26 28 30 32 71: 75 type=148 (RBDIHS) 26 28 30 33 71: 76 type=148 (RBDIHS) 29 28 30 31 71: 77 type=148 (RBDIHS) 29 28 30 32 71: 78 type=148 (RBDIHS) 29 28 30 33 71: 79 type=148 (RBDIHS) 34 28 30 31 71: 80 type=148 (RBDIHS) 34 28 30 32 71: 81 type=148 (RBDIHS) 34 28 30 33 71: 82 type=148 (RBDIHS) 26 28 34 35 71: 83 type=148 (RBDIHS) 26 28 34 36 71: 84 type=148 (RBDIHS) 26 28 34 37 71: 85 type=148 (RBDIHS) 29 28 34 35 71: 86 type=148 (RBDIHS) 29 28 34 36 71: 87 type=148 (RBDIHS) 29 28 34 37 71: 88 type=148 (RBDIHS) 30 28 34 35 71: 89 type=148 (RBDIHS) 30 28 34 36 71: 90 type=148 (RBDIHS) 30 28 34 37 71: 91 type=155 (RBDIHS) 26 38 40 41 71: 92 type=156 (RBDIHS) 26 38 40 42 71: 93 type=155 (RBDIHS) 39 38 40 41 71: 94 type=157 (RBDIHS) 39 38 40 42 71: 95 type=158 (RBDIHS) 38 40 42 44 71: 96 type=159 (RBDIHS) 38 40 42 58 71: 97 type=147 (RBDIHS) 40 42 44 45 71: 98 type=147 (RBDIHS) 40 42 44 46 71: 99 type=162 (RBDIHS) 40 42 44 47 71: 100 type=148 (RBDIHS) 43 42 44 45 71: 101 type=148 (RBDIHS) 43 42 44 46 71: 102 type=163 (RBDIHS) 43 42 44 47 71: 103 type=149 (RBDIHS) 58 42 44 45 71: 104 type=149 (RBDIHS) 58 42 44 46 71: 105 type=164 (RBDIHS) 58 42 44 47 71: 106 type=150 (RBDIHS) 40 42 58 60 71: 107 type=151 (RBDIHS) 44 42 58 60 71: 108 type=165 (RBDIHS) 44 47 48 49 71: 109 type=165 (RBDIHS) 44 47 48 52 71: 110 type=165 (RBDIHS) 50 47 48 49 71: 111 type=165 (RBDIHS) 50 47 48 52 71: 112 type=165 (RBDIHS) 44 47 50 51 71: 113 type=165 (RBDIHS) 44 47 50 54 71: 114 type=165 (RBDIHS) 48 47 50 51 71: 115 type=165 (RBDIHS) 48 47 50 54 71: 116 type=165 (RBDIHS) 47 48 52 53 71: 117 type=165 (RBDIHS) 47 48 52 56 71: 118 type=165 (RBDIHS) 49 48 52 53 71: 119 type=165 (RBDIHS) 49 48 52 56 71: 120 type=165 (RBDIHS) 47 50 54 55 71: 121 type=165 (RBDIHS) 47 50 54 56 71: 122 type=165 (RBDIHS) 51 50 54 55 71: 123 type=165 (RBDIHS) 51 50 54 56 71: 124 type=165 (RBDIHS) 48 52 56 54 71: 125 type=165 (RBDIHS) 48 52 56 57 71: 126 type=165 (RBDIHS) 53 52 56 54 71: 127 type=165 (RBDIHS) 53 52 56 57 71: 128 type=165 (RBDIHS) 50 54 56 52 71: 129 type=165 (RBDIHS) 50 54 56 57 71: 130 type=165 (RBDIHS) 55 54 56 52 71: 131 type=165 (RBDIHS) 55 54 56 57 71: 132 type=155 (RBDIHS) 42 58 60 61 71: 133 type=156 (RBDIHS) 42 58 60 62 71: 134 type=155 (RBDIHS) 59 58 60 61 71: 135 type=157 (RBDIHS) 59 58 60 62 71: 136 type=159 (RBDIHS) 58 60 62 65 71: 137 type=150 (RBDIHS) 60 62 65 67 71: 138 type=155 (RBDIHS) 62 65 67 68 71: 139 type=156 (RBDIHS) 62 65 67 69 71: 140 type=155 (RBDIHS) 66 65 67 68 71: 141 type=157 (RBDIHS) 66 65 67 69 71: 142 type=158 (RBDIHS) 65 67 69 71 71: 143 type=159 (RBDIHS) 65 67 69 89 71: 144 type=166 (RBDIHS) 67 69 71 74 71: 145 type=167 (RBDIHS) 89 69 71 74 71: 146 type=147 (RBDIHS) 67 69 71 72 71: 147 type=147 (RBDIHS) 67 69 71 73 71: 148 type=148 (RBDIHS) 70 69 71 72 71: 149 type=148 (RBDIHS) 70 69 71 73 71: 150 type=148 (RBDIHS) 70 69 71 74 71: 151 type=149 (RBDIHS) 89 69 71 72 71: 152 type=149 (RBDIHS) 89 69 71 73 71: 153 type=150 (RBDIHS) 67 69 89 91 71: 154 type=151 (RBDIHS) 71 69 89 91 71: 155 type=148 (RBDIHS) 69 71 74 75 71: 156 type=148 (RBDIHS) 69 71 74 76 71: 157 type=152 (RBDIHS) 69 71 74 77 71: 158 type=148 (RBDIHS) 72 71 74 75 71: 159 type=148 (RBDIHS) 72 71 74 76 71: 160 type=148 (RBDIHS) 72 71 74 77 71: 161 type=148 (RBDIHS) 73 71 74 75 71: 162 type=148 (RBDIHS) 73 71 74 76 71: 163 type=148 (RBDIHS) 73 71 74 77 71: 164 type=148 (RBDIHS) 71 74 77 78 71: 165 type=148 (RBDIHS) 71 74 77 79 71: 166 type=153 (RBDIHS) 71 74 77 80 71: 167 type=148 (RBDIHS) 75 74 77 78 71: 168 type=148 (RBDIHS) 75 74 77 79 71: 169 type=168 (RBDIHS) 75 74 77 80 71: 170 type=148 (RBDIHS) 76 74 77 78 71: 171 type=148 (RBDIHS) 76 74 77 79 71: 172 type=168 (RBDIHS) 76 74 77 80 71: 173 type=169 (RBDIHS) 74 77 80 81 71: 174 type=170 (RBDIHS) 74 77 80 82 71: 175 type=171 (RBDIHS) 78 77 80 82 71: 176 type=171 (RBDIHS) 79 77 80 82 71: 177 type=172 (RBDIHS) 77 80 82 83 71: 178 type=172 (RBDIHS) 77 80 82 86 71: 179 type=173 (RBDIHS) 81 80 82 83 71: 180 type=173 (RBDIHS) 81 80 82 86 71: 181 type=173 (RBDIHS) 80 82 83 84 71: 182 type=173 (RBDIHS) 80 82 83 85 71: 183 type=173 (RBDIHS) 86 82 83 84 71: 184 type=173 (RBDIHS) 86 82 83 85 71: 185 type=173 (RBDIHS) 80 82 86 87 71: 186 type=173 (RBDIHS) 80 82 86 88 71: 187 type=173 (RBDIHS) 83 82 86 87 71: 188 type=173 (RBDIHS) 83 82 86 88 71: 189 type=155 (RBDIHS) 69 89 91 92 71: 190 type=156 (RBDIHS) 69 89 91 93 71: 191 type=155 (RBDIHS) 90 89 91 92 71: 192 type=157 (RBDIHS) 90 89 91 93 71: 193 type=158 (RBDIHS) 89 91 93 95 71: 194 type=159 (RBDIHS) 89 91 93 100 71: 195 type=174 (RBDIHS) 91 93 95 98 71: 196 type=175 (RBDIHS) 100 93 95 98 71: 197 type=147 (RBDIHS) 91 93 95 96 71: 198 type=147 (RBDIHS) 91 93 95 97 71: 199 type=148 (RBDIHS) 94 93 95 96 71: 200 type=148 (RBDIHS) 94 93 95 97 71: 201 type=176 (RBDIHS) 94 93 95 98 71: 202 type=149 (RBDIHS) 100 93 95 96 71: 203 type=149 (RBDIHS) 100 93 95 97 71: 204 type=150 (RBDIHS) 91 93 100 102 71: 205 type=151 (RBDIHS) 95 93 100 102 71: 206 type=177 (RBDIHS) 93 95 98 99 71: 207 type=178 (RBDIHS) 96 95 98 99 71: 208 type=178 (RBDIHS) 97 95 98 99 71: 209 type=155 (RBDIHS) 93 100 102 103 71: 210 type=156 (RBDIHS) 93 100 102 104 71: 211 type=155 (RBDIHS) 101 100 102 103 71: 212 type=157 (RBDIHS) 101 100 102 104 71: 213 type=158 (RBDIHS) 100 102 104 106 71: 214 type=159 (RBDIHS) 100 102 104 115 71: 215 type=179 (RBDIHS) 102 104 106 109 71: 216 type=180 (RBDIHS) 115 104 106 109 71: 217 type=147 (RBDIHS) 102 104 106 107 71: 218 type=147 (RBDIHS) 102 104 106 108 71: 219 type=148 (RBDIHS) 105 104 106 107 71: 220 type=148 (RBDIHS) 105 104 106 108 71: 221 type=148 (RBDIHS) 105 104 106 109 71: 222 type=149 (RBDIHS) 115 104 106 107 71: 223 type=149 (RBDIHS) 115 104 106 108 71: 224 type=150 (RBDIHS) 102 104 115 117 71: 225 type=151 (RBDIHS) 106 104 115 117 71: 226 type=148 (RBDIHS) 104 106 109 110 71: 227 type=148 (RBDIHS) 104 106 109 111 71: 228 type=181 (RBDIHS) 104 106 109 112 71: 229 type=148 (RBDIHS) 107 106 109 110 71: 230 type=148 (RBDIHS) 107 106 109 111 71: 231 type=182 (RBDIHS) 107 106 109 112 71: 232 type=148 (RBDIHS) 108 106 109 110 71: 233 type=148 (RBDIHS) 108 106 109 111 71: 234 type=182 (RBDIHS) 108 106 109 112 71: 235 type=183 (RBDIHS) 106 109 112 113 71: 236 type=183 (RBDIHS) 106 109 112 114 71: 237 type=155 (RBDIHS) 104 115 117 118 71: 238 type=156 (RBDIHS) 104 115 117 119 71: 239 type=155 (RBDIHS) 116 115 117 118 71: 240 type=157 (RBDIHS) 116 115 117 119 71: 241 type=158 (RBDIHS) 115 117 119 121 71: 242 type=159 (RBDIHS) 115 117 119 134 71: 243 type=184 (RBDIHS) 117 119 121 124 71: 244 type=185 (RBDIHS) 134 119 121 124 71: 245 type=147 (RBDIHS) 117 119 121 122 71: 246 type=147 (RBDIHS) 117 119 121 123 71: 247 type=148 (RBDIHS) 120 119 121 122 71: 248 type=148 (RBDIHS) 120 119 121 123 71: 249 type=148 (RBDIHS) 120 119 121 124 71: 250 type=149 (RBDIHS) 134 119 121 122 71: 251 type=149 (RBDIHS) 134 119 121 123 71: 252 type=150 (RBDIHS) 117 119 134 136 71: 253 type=151 (RBDIHS) 121 119 134 136 71: 254 type=148 (RBDIHS) 119 121 124 125 71: 255 type=152 (RBDIHS) 119 121 124 126 71: 256 type=152 (RBDIHS) 119 121 124 130 71: 257 type=148 (RBDIHS) 122 121 124 125 71: 258 type=148 (RBDIHS) 122 121 124 126 71: 259 type=148 (RBDIHS) 122 121 124 130 71: 260 type=148 (RBDIHS) 123 121 124 125 71: 261 type=148 (RBDIHS) 123 121 124 126 71: 262 type=148 (RBDIHS) 123 121 124 130 71: 263 type=148 (RBDIHS) 121 124 126 127 71: 264 type=148 (RBDIHS) 121 124 126 128 71: 265 type=148 (RBDIHS) 121 124 126 129 71: 266 type=148 (RBDIHS) 125 124 126 127 71: 267 type=148 (RBDIHS) 125 124 126 128 71: 268 type=148 (RBDIHS) 125 124 126 129 71: 269 type=148 (RBDIHS) 130 124 126 127 71: 270 type=148 (RBDIHS) 130 124 126 128 71: 271 type=148 (RBDIHS) 130 124 126 129 71: 272 type=148 (RBDIHS) 121 124 130 131 71: 273 type=148 (RBDIHS) 121 124 130 132 71: 274 type=148 (RBDIHS) 121 124 130 133 71: 275 type=148 (RBDIHS) 125 124 130 131 71: 276 type=148 (RBDIHS) 125 124 130 132 71: 277 type=148 (RBDIHS) 125 124 130 133 71: 278 type=148 (RBDIHS) 126 124 130 131 71: 279 type=148 (RBDIHS) 126 124 130 132 71: 280 type=148 (RBDIHS) 126 124 130 133 71: 281 type=155 (RBDIHS) 119 134 136 137 71: 282 type=156 (RBDIHS) 119 134 136 138 71: 283 type=155 (RBDIHS) 135 134 136 137 71: 284 type=157 (RBDIHS) 135 134 136 138 71: 285 type=158 (RBDIHS) 134 136 138 140 71: 286 type=159 (RBDIHS) 134 136 138 144 71: 287 type=147 (RBDIHS) 136 138 140 141 71: 288 type=147 (RBDIHS) 136 138 140 142 71: 289 type=147 (RBDIHS) 136 138 140 143 71: 290 type=148 (RBDIHS) 139 138 140 141 71: 291 type=148 (RBDIHS) 139 138 140 142 71: 292 type=148 (RBDIHS) 139 138 140 143 71: 293 type=149 (RBDIHS) 144 138 140 141 71: 294 type=149 (RBDIHS) 144 138 140 142 71: 295 type=149 (RBDIHS) 144 138 140 143 71: 296 type=150 (RBDIHS) 136 138 144 146 71: 297 type=151 (RBDIHS) 140 138 144 146 71: 298 type=155 (RBDIHS) 138 144 146 147 71: 299 type=156 (RBDIHS) 138 144 146 148 71: 300 type=155 (RBDIHS) 145 144 146 147 71: 301 type=157 (RBDIHS) 145 144 146 148 71: 302 type=158 (RBDIHS) 144 146 148 150 71: 303 type=159 (RBDIHS) 144 146 148 154 71: 304 type=147 (RBDIHS) 146 148 150 151 71: 305 type=147 (RBDIHS) 146 148 150 152 71: 306 type=147 (RBDIHS) 146 148 150 153 71: 307 type=148 (RBDIHS) 149 148 150 151 71: 308 type=148 (RBDIHS) 149 148 150 152 71: 309 type=148 (RBDIHS) 149 148 150 153 71: 310 type=149 (RBDIHS) 154 148 150 151 71: 311 type=149 (RBDIHS) 154 148 150 152 71: 312 type=149 (RBDIHS) 154 148 150 153 71: Restr. Dih.: 71: nr: 0 71: CBT Dih.: 71: nr: 0 71: Fourier Dih.: 71: nr: 0 71: Improper Dih.: 71: nr: 0 71: Per. Imp. Dih.: 71: nr: 0 71: Tab. Dih.: 71: nr: 0 71: CMAP Dih.: 71: nr: 0 71: GB 1-2 Pol.: 71: nr: 0 71: GB 1-3 Pol.: 71: nr: 0 71: GB 1-4 Pol.: 71: nr: 0 71: GB Polariz.: 71: nr: 0 71: Nonpolar Sol.: 71: nr: 0 71: LJ-14: 71: nr: 1197 71: iatoms: 71: 0 type=186 (LJ14) 0 7 71: 1 type=186 (LJ14) 0 8 71: 2 type=187 (LJ14) 0 9 71: 3 type=188 (LJ14) 0 23 71: 4 type=189 (LJ14) 0 24 71: 5 type=190 (LJ14) 1 5 71: 6 type=190 (LJ14) 1 6 71: 7 type=190 (LJ14) 1 22 71: 8 type=190 (LJ14) 2 5 71: 9 type=190 (LJ14) 2 6 71: 10 type=190 (LJ14) 2 22 71: 11 type=190 (LJ14) 3 5 71: 12 type=190 (LJ14) 3 6 71: 13 type=190 (LJ14) 3 22 71: 14 type=191 (LJ14) 4 10 71: 15 type=191 (LJ14) 4 11 71: 16 type=192 (LJ14) 4 12 71: 17 type=190 (LJ14) 4 25 71: 18 type=192 (LJ14) 4 26 71: 19 type=193 (LJ14) 5 7 71: 20 type=193 (LJ14) 5 8 71: 21 type=191 (LJ14) 5 9 71: 22 type=194 (LJ14) 5 23 71: 23 type=186 (LJ14) 5 24 71: 24 type=191 (LJ14) 6 13 71: 25 type=191 (LJ14) 6 14 71: 26 type=192 (LJ14) 6 15 71: 27 type=195 (LJ14) 6 23 71: 28 type=187 (LJ14) 6 24 71: 29 type=193 (LJ14) 7 10 71: 30 type=193 (LJ14) 7 11 71: 31 type=191 (LJ14) 7 12 71: 32 type=196 (LJ14) 7 22 71: 33 type=193 (LJ14) 8 10 71: 34 type=193 (LJ14) 8 11 71: 35 type=191 (LJ14) 8 12 71: 36 type=196 (LJ14) 8 22 71: 37 type=191 (LJ14) 9 16 71: 38 type=191 (LJ14) 9 17 71: 39 type=187 (LJ14) 9 18 71: 40 type=197 (LJ14) 9 22 71: 41 type=193 (LJ14) 10 13 71: 42 type=193 (LJ14) 10 14 71: 43 type=191 (LJ14) 10 15 71: 44 type=193 (LJ14) 11 13 71: 45 type=193 (LJ14) 11 14 71: 46 type=191 (LJ14) 11 15 71: 47 type=190 (LJ14) 12 19 71: 48 type=190 (LJ14) 12 20 71: 49 type=190 (LJ14) 12 21 71: 50 type=193 (LJ14) 13 16 71: 51 type=193 (LJ14) 13 17 71: 52 type=186 (LJ14) 13 18 71: 53 type=193 (LJ14) 14 16 71: 54 type=193 (LJ14) 14 17 71: 55 type=186 (LJ14) 14 18 71: 56 type=190 (LJ14) 16 19 71: 57 type=190 (LJ14) 16 20 71: 58 type=190 (LJ14) 16 21 71: 59 type=190 (LJ14) 17 19 71: 60 type=190 (LJ14) 17 20 71: 61 type=190 (LJ14) 17 21 71: 62 type=196 (LJ14) 22 27 71: 63 type=197 (LJ14) 22 28 71: 64 type=198 (LJ14) 22 38 71: 65 type=190 (LJ14) 23 25 71: 66 type=195 (LJ14) 23 26 71: 67 type=186 (LJ14) 24 29 71: 68 type=187 (LJ14) 24 30 71: 69 type=187 (LJ14) 24 34 71: 70 type=188 (LJ14) 24 39 71: 71 type=189 (LJ14) 24 40 71: 72 type=190 (LJ14) 25 27 71: 73 type=190 (LJ14) 25 28 71: 74 type=190 (LJ14) 25 38 71: 75 type=191 (LJ14) 26 31 71: 76 type=191 (LJ14) 26 32 71: 77 type=191 (LJ14) 26 33 71: 78 type=191 (LJ14) 26 35 71: 79 type=191 (LJ14) 26 36 71: 80 type=191 (LJ14) 26 37 71: 81 type=190 (LJ14) 26 41 71: 82 type=192 (LJ14) 26 42 71: 83 type=193 (LJ14) 27 29 71: 84 type=191 (LJ14) 27 30 71: 85 type=191 (LJ14) 27 34 71: 86 type=194 (LJ14) 27 39 71: 87 type=186 (LJ14) 27 40 71: 88 type=195 (LJ14) 28 39 71: 89 type=187 (LJ14) 28 40 71: 90 type=193 (LJ14) 29 31 71: 91 type=193 (LJ14) 29 32 71: 92 type=193 (LJ14) 29 33 71: 93 type=193 (LJ14) 29 35 71: 94 type=193 (LJ14) 29 36 71: 95 type=193 (LJ14) 29 37 71: 96 type=196 (LJ14) 29 38 71: 97 type=191 (LJ14) 30 35 71: 98 type=191 (LJ14) 30 36 71: 99 type=191 (LJ14) 30 37 71: 100 type=197 (LJ14) 30 38 71: 101 type=191 (LJ14) 31 34 71: 102 type=191 (LJ14) 32 34 71: 103 type=191 (LJ14) 33 34 71: 104 type=197 (LJ14) 34 38 71: 105 type=196 (LJ14) 38 43 71: 106 type=197 (LJ14) 38 44 71: 107 type=198 (LJ14) 38 58 71: 108 type=190 (LJ14) 39 41 71: 109 type=195 (LJ14) 39 42 71: 110 type=186 (LJ14) 40 45 71: 111 type=186 (LJ14) 40 46 71: 112 type=199 (LJ14) 40 47 71: 113 type=188 (LJ14) 40 59 71: 114 type=189 (LJ14) 40 60 71: 115 type=190 (LJ14) 41 43 71: 116 type=190 (LJ14) 41 44 71: 117 type=190 (LJ14) 41 58 71: 118 type=200 (LJ14) 42 48 71: 119 type=200 (LJ14) 42 50 71: 120 type=190 (LJ14) 42 61 71: 121 type=192 (LJ14) 42 62 71: 122 type=193 (LJ14) 43 45 71: 123 type=193 (LJ14) 43 46 71: 124 type=201 (LJ14) 43 47 71: 125 type=194 (LJ14) 43 59 71: 126 type=186 (LJ14) 43 60 71: 127 type=202 (LJ14) 44 49 71: 128 type=202 (LJ14) 44 51 71: 129 type=200 (LJ14) 44 52 71: 130 type=200 (LJ14) 44 54 71: 131 type=195 (LJ14) 44 59 71: 132 type=187 (LJ14) 44 60 71: 133 type=201 (LJ14) 45 48 71: 134 type=201 (LJ14) 45 50 71: 135 type=196 (LJ14) 45 58 71: 136 type=201 (LJ14) 46 48 71: 137 type=201 (LJ14) 46 50 71: 138 type=196 (LJ14) 46 58 71: 139 type=203 (LJ14) 47 53 71: 140 type=203 (LJ14) 47 55 71: 141 type=204 (LJ14) 47 56 71: 142 type=205 (LJ14) 47 58 71: 143 type=203 (LJ14) 48 51 71: 144 type=204 (LJ14) 48 54 71: 145 type=203 (LJ14) 48 57 71: 146 type=203 (LJ14) 49 50 71: 147 type=206 (LJ14) 49 53 71: 148 type=203 (LJ14) 49 56 71: 149 type=204 (LJ14) 50 52 71: 150 type=203 (LJ14) 50 57 71: 151 type=206 (LJ14) 51 55 71: 152 type=203 (LJ14) 51 56 71: 153 type=203 (LJ14) 52 55 71: 154 type=203 (LJ14) 53 54 71: 155 type=206 (LJ14) 53 57 71: 156 type=206 (LJ14) 55 57 71: 157 type=196 (LJ14) 58 63 71: 158 type=196 (LJ14) 58 64 71: 159 type=198 (LJ14) 58 65 71: 160 type=190 (LJ14) 59 61 71: 161 type=195 (LJ14) 59 62 71: 162 type=188 (LJ14) 60 66 71: 163 type=189 (LJ14) 60 67 71: 164 type=190 (LJ14) 61 63 71: 165 type=190 (LJ14) 61 64 71: 166 type=190 (LJ14) 61 65 71: 167 type=190 (LJ14) 62 68 71: 168 type=192 (LJ14) 62 69 71: 169 type=194 (LJ14) 63 66 71: 170 type=186 (LJ14) 63 67 71: 171 type=194 (LJ14) 64 66 71: 172 type=186 (LJ14) 64 67 71: 173 type=196 (LJ14) 65 70 71: 174 type=197 (LJ14) 65 71 71: 175 type=198 (LJ14) 65 89 71: 176 type=190 (LJ14) 66 68 71: 177 type=195 (LJ14) 66 69 71: 178 type=186 (LJ14) 67 72 71: 179 type=186 (LJ14) 67 73 71: 180 type=187 (LJ14) 67 74 71: 181 type=188 (LJ14) 67 90 71: 182 type=189 (LJ14) 67 91 71: 183 type=190 (LJ14) 68 70 71: 184 type=190 (LJ14) 68 71 71: 185 type=190 (LJ14) 68 89 71: 186 type=191 (LJ14) 69 75 71: 187 type=191 (LJ14) 69 76 71: 188 type=192 (LJ14) 69 77 71: 189 type=190 (LJ14) 69 92 71: 190 type=192 (LJ14) 69 93 71: 191 type=193 (LJ14) 70 72 71: 192 type=193 (LJ14) 70 73 71: 193 type=191 (LJ14) 70 74 71: 194 type=194 (LJ14) 70 90 71: 195 type=186 (LJ14) 70 91 71: 196 type=191 (LJ14) 71 78 71: 197 type=191 (LJ14) 71 79 71: 198 type=187 (LJ14) 71 80 71: 199 type=195 (LJ14) 71 90 71: 200 type=187 (LJ14) 71 91 71: 201 type=193 (LJ14) 72 75 71: 202 type=193 (LJ14) 72 76 71: 203 type=191 (LJ14) 72 77 71: 204 type=196 (LJ14) 72 89 71: 205 type=193 (LJ14) 73 75 71: 206 type=193 (LJ14) 73 76 71: 207 type=191 (LJ14) 73 77 71: 208 type=196 (LJ14) 73 89 71: 209 type=190 (LJ14) 74 81 71: 210 type=207 (LJ14) 74 82 71: 211 type=197 (LJ14) 74 89 71: 212 type=193 (LJ14) 75 78 71: 213 type=193 (LJ14) 75 79 71: 214 type=186 (LJ14) 75 80 71: 215 type=193 (LJ14) 76 78 71: 216 type=193 (LJ14) 76 79 71: 217 type=186 (LJ14) 76 80 71: 218 type=187 (LJ14) 77 83 71: 219 type=187 (LJ14) 77 86 71: 220 type=190 (LJ14) 78 81 71: 221 type=208 (LJ14) 78 82 71: 222 type=190 (LJ14) 79 81 71: 223 type=208 (LJ14) 79 82 71: 224 type=190 (LJ14) 80 84 71: 225 type=190 (LJ14) 80 85 71: 226 type=190 (LJ14) 80 87 71: 227 type=190 (LJ14) 80 88 71: 228 type=190 (LJ14) 81 83 71: 229 type=190 (LJ14) 81 86 71: 230 type=190 (LJ14) 83 87 71: 231 type=190 (LJ14) 83 88 71: 232 type=190 (LJ14) 84 86 71: 233 type=190 (LJ14) 85 86 71: 234 type=196 (LJ14) 89 94 71: 235 type=197 (LJ14) 89 95 71: 236 type=198 (LJ14) 89 100 71: 237 type=190 (LJ14) 90 92 71: 238 type=195 (LJ14) 90 93 71: 239 type=186 (LJ14) 91 96 71: 240 type=186 (LJ14) 91 97 71: 241 type=209 (LJ14) 91 98 71: 242 type=188 (LJ14) 91 101 71: 243 type=189 (LJ14) 91 102 71: 244 type=190 (LJ14) 92 94 71: 245 type=190 (LJ14) 92 95 71: 246 type=190 (LJ14) 92 100 71: 247 type=190 (LJ14) 93 99 71: 248 type=190 (LJ14) 93 103 71: 249 type=192 (LJ14) 93 104 71: 250 type=193 (LJ14) 94 96 71: 251 type=193 (LJ14) 94 97 71: 252 type=210 (LJ14) 94 98 71: 253 type=194 (LJ14) 94 101 71: 254 type=186 (LJ14) 94 102 71: 255 type=195 (LJ14) 95 101 71: 256 type=187 (LJ14) 95 102 71: 257 type=190 (LJ14) 96 99 71: 258 type=196 (LJ14) 96 100 71: 259 type=190 (LJ14) 97 99 71: 260 type=196 (LJ14) 97 100 71: 261 type=211 (LJ14) 98 100 71: 262 type=196 (LJ14) 100 105 71: 263 type=197 (LJ14) 100 106 71: 264 type=198 (LJ14) 100 115 71: 265 type=190 (LJ14) 101 103 71: 266 type=195 (LJ14) 101 104 71: 267 type=186 (LJ14) 102 107 71: 268 type=186 (LJ14) 102 108 71: 269 type=187 (LJ14) 102 109 71: 270 type=188 (LJ14) 102 116 71: 271 type=189 (LJ14) 102 117 71: 272 type=190 (LJ14) 103 105 71: 273 type=190 (LJ14) 103 106 71: 274 type=190 (LJ14) 103 115 71: 275 type=191 (LJ14) 104 110 71: 276 type=191 (LJ14) 104 111 71: 277 type=197 (LJ14) 104 112 71: 278 type=190 (LJ14) 104 118 71: 279 type=192 (LJ14) 104 119 71: 280 type=193 (LJ14) 105 107 71: 281 type=193 (LJ14) 105 108 71: 282 type=191 (LJ14) 105 109 71: 283 type=194 (LJ14) 105 116 71: 284 type=186 (LJ14) 105 117 71: 285 type=195 (LJ14) 106 113 71: 286 type=195 (LJ14) 106 114 71: 287 type=195 (LJ14) 106 116 71: 288 type=187 (LJ14) 106 117 71: 289 type=193 (LJ14) 107 110 71: 290 type=193 (LJ14) 107 111 71: 291 type=196 (LJ14) 107 112 71: 292 type=196 (LJ14) 107 115 71: 293 type=193 (LJ14) 108 110 71: 294 type=193 (LJ14) 108 111 71: 295 type=196 (LJ14) 108 112 71: 296 type=196 (LJ14) 108 115 71: 297 type=197 (LJ14) 109 115 71: 298 type=194 (LJ14) 110 113 71: 299 type=194 (LJ14) 110 114 71: 300 type=194 (LJ14) 111 113 71: 301 type=194 (LJ14) 111 114 71: 302 type=196 (LJ14) 115 120 71: 303 type=197 (LJ14) 115 121 71: 304 type=198 (LJ14) 115 134 71: 305 type=190 (LJ14) 116 118 71: 306 type=195 (LJ14) 116 119 71: 307 type=186 (LJ14) 117 122 71: 308 type=186 (LJ14) 117 123 71: 309 type=187 (LJ14) 117 124 71: 310 type=188 (LJ14) 117 135 71: 311 type=189 (LJ14) 117 136 71: 312 type=190 (LJ14) 118 120 71: 313 type=190 (LJ14) 118 121 71: 314 type=190 (LJ14) 118 134 71: 315 type=191 (LJ14) 119 125 71: 316 type=192 (LJ14) 119 126 71: 317 type=192 (LJ14) 119 130 71: 318 type=190 (LJ14) 119 137 71: 319 type=192 (LJ14) 119 138 71: 320 type=193 (LJ14) 120 122 71: 321 type=193 (LJ14) 120 123 71: 322 type=191 (LJ14) 120 124 71: 323 type=194 (LJ14) 120 135 71: 324 type=186 (LJ14) 120 136 71: 325 type=191 (LJ14) 121 127 71: 326 type=191 (LJ14) 121 128 71: 327 type=191 (LJ14) 121 129 71: 328 type=191 (LJ14) 121 131 71: 329 type=191 (LJ14) 121 132 71: 330 type=191 (LJ14) 121 133 71: 331 type=195 (LJ14) 121 135 71: 332 type=187 (LJ14) 121 136 71: 333 type=193 (LJ14) 122 125 71: 334 type=191 (LJ14) 122 126 71: 335 type=191 (LJ14) 122 130 71: 336 type=196 (LJ14) 122 134 71: 337 type=193 (LJ14) 123 125 71: 338 type=191 (LJ14) 123 126 71: 339 type=191 (LJ14) 123 130 71: 340 type=196 (LJ14) 123 134 71: 341 type=197 (LJ14) 124 134 71: 342 type=193 (LJ14) 125 127 71: 343 type=193 (LJ14) 125 128 71: 344 type=193 (LJ14) 125 129 71: 345 type=193 (LJ14) 125 131 71: 346 type=193 (LJ14) 125 132 71: 347 type=193 (LJ14) 125 133 71: 348 type=191 (LJ14) 126 131 71: 349 type=191 (LJ14) 126 132 71: 350 type=191 (LJ14) 126 133 71: 351 type=191 (LJ14) 127 130 71: 352 type=191 (LJ14) 128 130 71: 353 type=191 (LJ14) 129 130 71: 354 type=196 (LJ14) 134 139 71: 355 type=197 (LJ14) 134 140 71: 356 type=198 (LJ14) 134 144 71: 357 type=190 (LJ14) 135 137 71: 358 type=195 (LJ14) 135 138 71: 359 type=186 (LJ14) 136 141 71: 360 type=186 (LJ14) 136 142 71: 361 type=186 (LJ14) 136 143 71: 362 type=188 (LJ14) 136 145 71: 363 type=189 (LJ14) 136 146 71: 364 type=190 (LJ14) 137 139 71: 365 type=190 (LJ14) 137 140 71: 366 type=190 (LJ14) 137 144 71: 367 type=190 (LJ14) 138 147 71: 368 type=192 (LJ14) 138 148 71: 369 type=193 (LJ14) 139 141 71: 370 type=193 (LJ14) 139 142 71: 371 type=193 (LJ14) 139 143 71: 372 type=194 (LJ14) 139 145 71: 373 type=186 (LJ14) 139 146 71: 374 type=195 (LJ14) 140 145 71: 375 type=187 (LJ14) 140 146 71: 376 type=196 (LJ14) 141 144 71: 377 type=196 (LJ14) 142 144 71: 378 type=196 (LJ14) 143 144 71: 379 type=196 (LJ14) 144 149 71: 380 type=197 (LJ14) 144 150 71: 381 type=198 (LJ14) 144 154 71: 382 type=190 (LJ14) 145 147 71: 383 type=195 (LJ14) 145 148 71: 384 type=186 (LJ14) 146 151 71: 385 type=186 (LJ14) 146 152 71: 386 type=186 (LJ14) 146 153 71: 387 type=188 (LJ14) 146 155 71: 388 type=190 (LJ14) 147 149 71: 389 type=190 (LJ14) 147 150 71: 390 type=190 (LJ14) 147 154 71: 391 type=193 (LJ14) 149 151 71: 392 type=193 (LJ14) 149 152 71: 393 type=193 (LJ14) 149 153 71: 394 type=194 (LJ14) 149 155 71: 395 type=195 (LJ14) 150 155 71: 396 type=196 (LJ14) 151 154 71: 397 type=196 (LJ14) 152 154 71: 398 type=196 (LJ14) 153 154 71: Coulomb-14: 71: nr: 0 71: LJC-14 q: 71: nr: 0 71: LJC Pairs NB: 71: nr: 0 71: LJ (SR): 71: nr: 0 71: Buck.ham (SR): 71: nr: 0 71: LJ: 71: nr: 0 71: B.ham: 71: nr: 0 71: Disper. corr.: 71: nr: 0 71: Coulomb (SR): 71: nr: 0 71: Coul: 71: nr: 0 71: RF excl.: 71: nr: 0 71: Coul. recip.: 71: nr: 0 71: LJ recip.: 71: nr: 0 71: DPD: 71: nr: 0 71: Polarization: 71: nr: 0 71: Water Pol.: 71: nr: 0 71: Thole Pol.: 71: nr: 0 71: Anharm. Pol.: 71: nr: 0 71: Position Rest.: 71: nr: 0 71: Flat-b. P-R.: 71: nr: 0 71: Dis. Rest.: 71: nr: 0 71: D.R.Viol. (nm): 71: nr: 0 71: Orient. Rest.: 71: nr: 0 71: Ori. R. RMSD: 71: nr: 0 71: Angle Rest.: 71: nr: 0 71: Angle Rest. Z: 71: nr: 0 71: Dih. Rest.: 71: nr: 0 71: Dih. Rest. Vi.: 71: nr: 0 71: Constraint: 71: nr: 0 71: Constr. No Co.: 71: nr: 0 71: Settle: 71: nr: 0 71: Virtual site 1: 71: nr: 0 71: Virtual site 2: 71: nr: 0 71: Virt. site 2fd: 71: nr: 0 71: Virtual site 3: 71: nr: 0 71: Virt. site 3fd: 71: nr: 0 71: Vir. site 3fad: 71: nr: 0 71: Vir. site 3out: 71: nr: 0 71: Virt. site 4fd: 71: nr: 0 71: Vir. site 4fdn: 71: nr: 0 71: Virtual site N: 71: nr: 0 71: COM Pull En.: 71: nr: 0 71: Dens. fitting: 71: nr: 0 71: Quantum En.: 71: nr: 0 71: NN Potential: 71: nr: 0 71: Potential: 71: nr: 0 71: Kinetic En.: 71: nr: 0 71: Total Energy: 71: nr: 0 71: Conserved En.: 71: nr: 0 71: Temperature: 71: nr: 0 71: Vir. Temp.: 71: nr: 0 71: Pres. DC: 71: nr: 0 71: Pressure: 71: nr: 0 71: dH/dl constr.: 71: nr: 0 71: dVremain/dl: 71: nr: 0 71: dEkin/dl: 71: nr: 0 71: dVcoul/dl: 71: nr: 0 71: dVvdw/dl: 71: nr: 0 71: dVbonded/dl: 71: nr: 0 71: dVrestraint/dl: 71: nr: 0 71: dVtemp/dl: 71: nr: 0 71: grp[T-Coupling ] nr=1, name=[ rest] 71: grp[Energy Mon. ] nr=1, name=[ rest] 71: grp[Acc. not used] nr=1, name=[ rest] 71: grp[Freeze ] nr=1, name=[ rest] 71: grp[User1 ] nr=1, name=[ rest] 71: grp[User2 ] nr=1, name=[ rest] 71: grp[VCM ] nr=1, name=[ rest] 71: grp[Compressed X] nr=1, name=[ rest] 71: grp[Or. Res. Fit] nr=1, name=[ rest] 71: grp[QMMM ] nr=1, name=[ rest] 71: grpname (11): 71: grpname[0]={name="System"} 71: grpname[1]={name="Protein"} 71: grpname[2]={name="Protein-H"} 71: grpname[3]={name="C-alpha"} 71: grpname[4]={name="Backbone"} 71: grpname[5]={name="MainChain"} 71: grpname[6]={name="MainChain+Cb"} 71: grpname[7]={name="MainChain+H"} 71: grpname[8]={name="SideChain"} 71: grpname[9]={name="SideChain-H"} 71: grpname[10]={name="rest"} 71: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 71: allocated 0 0 0 0 0 0 0 0 0 0 71: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 71: box (3x3): 71: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 71: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 71: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 71: box_rel (3x3): 71: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: boxv (3x3): 71: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: pres_prev (3x3): 71: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: svir_prev (3x3): 71: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: fvir_prev (3x3): 71: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: nosehoover_xi: not available 71: x (156x3): 71: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 71: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 71: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 71: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 71: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 71: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 71: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 71: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 71: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 71: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 71: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 71: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 71: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 71: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 71: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 71: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 71: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 71: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 71: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 71: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 71: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 71: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 71: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 71: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 71: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 71: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 71: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 71: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 71: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 71: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 71: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 71: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 71: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 71: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 71: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 71: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 71: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 71: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 71: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 71: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 71: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 71: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 71: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 71: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 71: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 71: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 71: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 71: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 71: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 71: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 71: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 71: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 71: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 71: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 71: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 71: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 71: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 71: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 71: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 71: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 71: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 71: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 71: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 71: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 71: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 71: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 71: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 71: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 71: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 71: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 71: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 71: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 71: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 71: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 71: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 71: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 71: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 71: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 71: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 71: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 71: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 71: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 71: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 71: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 71: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 71: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 71: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 71: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 71: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 71: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 71: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 71: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 71: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 71: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 71: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 71: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 71: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 71: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 71: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 71: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 71: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 71: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 71: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 71: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 71: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 71: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 71: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 71: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 71: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 71: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 71: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 71: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 71: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 71: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 71: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 71: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 71: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 71: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 71: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 71: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 71: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 71: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 71: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 71: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 71: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 71: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 71: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 71: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 71: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 71: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 71: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 71: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 71: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 71: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 71: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 71: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 71: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 71: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 71: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 71: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 71: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 71: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 71: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 71: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 71: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 71: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 71: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 71: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 71: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 71: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 71: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 71: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 71: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 71: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 71: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 71: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 71: v (156x3): 71: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 71: Group statistics 71: T-Coupling : 156 (total 156 atoms) 71: Energy Mon. : 156 (total 156 atoms) 71: Acc. not used: 156 (total 156 atoms) 71: Freeze : 156 (total 156 atoms) 71: User1 : 156 (total 156 atoms) 71: User2 : 156 (total 156 atoms) 71: VCM : 156 (total 156 atoms) 71: Compressed X: 156 (total 156 atoms) 71: Or. Res. Fit: 156 (total 156 atoms) 71: QMMM : 156 (total 156 atoms) 71: [ OK ] DumpTest.WorksWithTpr (15 ms) 71: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: [ OK ] DumpTest.WorksWithTprAndMdpWriting (2 ms) 71: [----------] 2 tests from DumpTest (17 ms total) 71: 71: [----------] 3 tests from HelpwritingTest 71: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 71: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 71: [ RUN ] HelpwritingTest.DumpWritesHelp 71: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 71: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 71: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 71: [----------] 3 tests from HelpwritingTest (1 ms total) 71: 71: [----------] 7 tests from GmxMakeNdx 71: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 71: 71: Reading structure file 71: Going to read 0 old index file(s) 71: Analysing residue names: 71: There are: 16 Protein residues 71: Analysing Protein... 71: 71: 0 System : 256 atoms 71: 1 Protein : 256 atoms 71: 2 Protein-H : 139 atoms 71: 3 C-alpha : 16 atoms 71: 4 Backbone : 48 atoms 71: 5 MainChain : 63 atoms 71: 6 MainChain+Cb : 78 atoms 71: 7 MainChain+H : 81 atoms 71: 8 SideChain : 175 atoms 71: 9 SideChain-H : 76 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (54 ms) 71: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 71: Going to read 1 old index file(s) 71: Deducing 22 atoms in the system from indices in the index file 71: 71: 0 System : 22 atoms 71: 1 Protein : 22 atoms 71: 2 Protein-H : 10 atoms 71: 3 C-alpha : 1 atoms 71: 4 Backbone : 5 atoms 71: 5 MainChain : 7 atoms 71: 6 MainChain+Cb : 8 atoms 71: 7 MainChain+H : 9 atoms 71: 8 SideChain : 13 atoms 71: 9 SideChain-H : 3 atoms 71: 10 CA : 1 atoms 71: 11 C_&_r_1 : 1 atoms 71: 12 C_&_r_2 : 1 atoms 71: 13 N_&_r_2 : 1 atoms 71: 14 N_&_r_3 : 1 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: Copied index group 1 'Protein' 71: Copied index group 2 'Protein-H' 71: Merged two groups with OR: 22 10 -> 22 71: 71: > 71: [ OK ] GmxMakeNdx.HandlesNoStructureInput (1 ms) 71: [ RUN ] GmxMakeNdx.HandlesNotProtein 71: Going to read 1 old index file(s) 71: Deducing 6 atoms in the system from indices in the index file 71: 71: 0 System : 6 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: [ OK ] GmxMakeNdx.HandlesNotProtein (1 ms) 71: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 71: Going to read 1 old index file(s) 71: Deducing 22 atoms in the system from indices in the index file 71: 71: 0 System : 22 atoms 71: 1 Protein : 22 atoms 71: 2 Protein-H : 10 atoms 71: 3 C-alpha : 1 atoms 71: 4 Backbone : 5 atoms 71: 5 MainChain : 7 atoms 71: 6 MainChain+Cb : 8 atoms 71: 7 MainChain+H : 9 atoms 71: 8 SideChain : 13 atoms 71: 9 SideChain-H : 3 atoms 71: 10 CA : 1 atoms 71: 11 C_&_r_1 : 1 atoms 71: 12 C_&_r_2 : 1 atoms 71: 13 N_&_r_2 : 1 atoms 71: 14 N_&_r_3 : 1 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: Copied index group 4 'Backbone' 71: Copied index group 8 'SideChain' 71: Merged two groups with AND: 5 13 -> 0 71: Group is empty 71: 71: > 71: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (1 ms) 71: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 71: Going to read 1 old index file(s) 71: Deducing 6 atoms in the system from indices in the index file 71: 71: 0 System : 6 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: Removed group 0 'System' 71: 71: > 71: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 71: [ RUN ] GmxMakeNdx.Splitres 71: 71: Reading structure file 71: Going to read 0 old index file(s) 71: Analysing residue names: 71: There are: 2 Water residues 71: 71: 0 System : 6 atoms 71: 1 Water : 6 atoms 71: 2 SOL : 6 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: Splitting group 1 'Water' into residues 71: 71: > 71: [ OK ] GmxMakeNdx.Splitres (1 ms) 71: [ RUN ] GmxMakeNdx.Splitat 71: 71: Reading structure file 71: Going to read 0 old index file(s) 71: Analysing residue names: 71: There are: 2 Water residues 71: 71: 0 System : 6 atoms 71: 1 Water : 6 atoms 71: 2 SOL : 6 atoms 71: 71: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 71: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 71: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 71: 'r': residue 'res' nr 'chain' char 71: "name": group 'case': case sensitive 'q': save and quit 71: 'ri': residue index 71: 71: > 71: Splitting group 1 'Water' into atoms 71: 71: > 71: [ OK ] GmxMakeNdx.Splitat (1 ms) 71: [----------] 7 tests from GmxMakeNdx (63 ms total) 71: 71: [----------] 4 tests from ReportMethodsTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Setting the LD random seed to -155267957 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 71: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 71: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 71: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 71: [ RUN ] ReportMethodsTest.WritesCorrectInformation 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: [ OK ] ReportMethodsTest.WritesCorrectInformation (1 ms) 71: [ RUN ] ReportMethodsTest.ToolEndToEndTest 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: section: Methods 71: subsection: Simulation system 71: A system of 1 molecules (156 atoms) was simulated. 71: 71: subsection: Simulation settings 71: A total of 0 ns were simulated with a time step of 1 fs. 71: Neighbor searching was performed every 10 steps. 71: The Cut-off algorithm was used for electrostatic interactions. 71: with a cut-off of 1 nm. 71: A single cut-off of 1.1 nm was used for Van der Waals interactions. 71: [ OK ] ReportMethodsTest.ToolEndToEndTest (14 ms) 71: [----------] 4 tests from ReportMethodsTest (16 ms total) 71: 71: [----------] 4 tests from ConvertTprTest 71: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Setting the LD random seed to -1625899269 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: Input file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 0 71: Runtime for the run 0 ps 71: Run end step 0 71: Run end time 0 ps 71: 71: Extending remaining runtime by 100 ps 71: 71: Output file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 100000 71: Runtime for the run 100 ps 71: Run end step 100000 71: Run end time 100 ps 71: 71: Input file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 100000 71: Runtime for the run 100 ps 71: Run end step 100000 71: Run end time 100 ps 71: 71: Extending remaining runtime by 100 ps 71: 71: Output file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 200000 71: Runtime for the run 200 ps 71: Run end step 200000 71: Run end time 200 ps 71: 71: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (1034 ms) 71: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Setting the LD random seed to -72681738 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: Input file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 0 71: Runtime for the run 0 ps 71: Run end step 0 71: Run end time 0 ps 71: 71: Extending remaining runtime to 100 ps 71: 71: Output file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 100000 71: Runtime for the run 100 ps 71: Run end step 100000 71: Run end time 100 ps 71: 71: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (1024 ms) 71: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Setting nsteps to 102 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Setting the LD random seed to -152322305 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: Input file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 0 71: Runtime for the run 0 ps 71: Run end step 0 71: Run end time 0 ps 71: 71: 71: Output file: 71: Run start step 0 71: Run start time 0 ps 71: Step to be made during run 102 71: Runtime for the run 0.102 ps 71: Run end step 102 71: Run end time 0.102 ps 71: 71: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (1024 ms) 71: [ RUN ] ConvertTprTest.generateVelocitiesTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Setting the LD random seed to 1073740763 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: 71: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] ConvertTprTest.generateVelocitiesTest (1082 ms) 71: [----------] 4 tests from ConvertTprTest (4167 ms total) 71: 71: [----------] 1 test from ConvertTprNoVelocityTest 71: [ RUN ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 2 [file lysozyme.top, line 1465]: 71: System has non-zero total charge: 2.000000 71: Total charge should normally be an integer. See 71: https://manual.gromacs.org/current/user-guide/floating-point.html 71: for discussion on how close it should be to an integer. 71: 71: 71: 71: 71: NOTE 3 [file lysozyme.top, line 1465]: 71: Zero-step energy minimization will alter the coordinates before 71: calculating the energy. If you just want the energy of a single point, 71: try zero-step MD (with unconstrained_start = yes). To do multiple 71: single-point energy evaluations of different configurations of the same 71: topology, use mdrun -rerun. 71: 71: Number of degrees of freedom in T-Coupling group rest is 465.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 71: Setting the LD random seed to -86023265 71: 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 71: Analysing residue names: 71: There are: 10 Protein residues 71: Analysing Protein... 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] ConvertTprNoVelocityTest.refuseToGenerateVelocitiesWhenTprDidNotHaveVelocitiesInitiallyTest (1040 ms) 71: [----------] 1 test from ConvertTprNoVelocityTest (1040 ms total) 71: 71: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: trr version: GMX_trn_file (single precision) 71: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (38 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (2 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 71: ./src/gromacs/tools/tests/trjconv.cpp:86: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md (0 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (2 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 71: Will write trr: Trajectory in portable xdr format 71: Group 0 ( System) has 6 elements 71: Group 1 (FirstWaterMolecule) has 3 elements 71: Group 2 (SecondWaterMolecule) has 3 elements 71: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 71: -> frame 1 time 1.000 71: Last written: frame 1 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: Select group for output 71: Selected 2: 'SecondWaterMolecule' 71: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (1 ms) 71: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 71: ./src/gromacs/tools/tests/trjconv.cpp:123: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md (0 ms) 71: [----------] 14 tests from Works/TrjconvWithDifferentInputFormats (56 ms total) 71: 71: [----------] 35 tests from Works/TrjconvDumpTest 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 71: Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 71: Precision of /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 71: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 71: Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 0 ps 71: -> frame 0 time 0.000 71: Last written: frame 0 time 0.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 71: Will write trr: Trajectory in portable xdr format 71: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 71: 71: Dumping frame at t= 1 ps 71: -> frame 0 time 1.000 71: Last written: frame 0 time 1.000 71: 71: 71: Note that major changes are planned in future for trjconv, to improve usability and utility. 71: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (1 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 71: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 71: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 71: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 71: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 (0 ms) 71: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 71: ./src/gromacs/tools/tests/trjconv.cpp:196: Skipped 71: Cannot test H5MD reading if H5MD support is not configured 71: 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 (0 ms) 71: [----------] 35 tests from Works/TrjconvDumpTest (31 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 70 tests from 8 test suites ran. (7477 ms total) 71: [ PASSED ] 63 tests. 71: [ SKIPPED ] 7 tests, listed below: 71: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_h5md 71: [ SKIPPED ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_h5md 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time__1_00 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_00 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_0_30 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_1_00 71: [ SKIPPED ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_h5md_dump_time_999999_00 71/103 Test #71: ToolUnitTests ............................. Passed 7.51 sec test 72 Start 72: ToolWithLeaksUnitTests 72: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/tool-test-with-leaks "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/ToolWithLeaksUnitTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests 72: Test timeout computed to be: 1920 72: [==========] Running 2 tests from 2 test suites. 72: [----------] Global test environment set-up. 72: [----------] 1 test from ConvertTprTest 72: [ RUN ] ConvertTprTest.selectIndexTest 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 72: NVE simulation with an initial temperature of zero: will use a Verlet 72: buffer of 10%. Check your energy drift! 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 72: Group 0 ( System) has 156 elements 72: Group 1 ( Protein) has 156 elements 72: Group 2 ( Protein-H) has 75 elements 72: Group 3 ( C-alpha) has 10 elements 72: Group 4 ( Backbone) has 30 elements 72: Group 5 ( MainChain) has 40 elements 72: Group 6 ( MainChain+Cb) has 49 elements 72: Group 7 ( MainChain+H) has 52 elements 72: Group 8 ( SideChain) has 104 elements 72: Group 9 ( SideChain-H) has 35 elements 72: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 72: Reduced ilist BONDS from 156 to 75 entries 72: Reduced ilist ANGLES from 281 to 98 entries 72: Reduced ilist PDIHS from 29 to 12 entries 72: Reduced ilist RBDIHS from 313 to 89 entries 72: Reduced ilist LJ14 from 399 to 107 entries 72: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_selectIndexTest_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 72: Setting the LD random seed to 1475067817 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: 72: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/lysozyme.pdb', all velocities are zero 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Selected 2: 'Protein-H' 72: [ OK ] ConvertTprTest.selectIndexTest (1042 ms) 72: [----------] 1 test from ConvertTprTest (1042 ms total) 72: 72: [----------] 1 test from ConvertTprNoVelocityTest 72: [ RUN ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 72: For a correct single-point energy evaluation with nsteps = 0, use 72: continuation = yes to avoid constraining the input coordinates. 72: 72: Generating 1-4 interactions: fudge = 0.5 72: 72: NOTE 2 [file lysozyme.top, line 1465]: 72: System has non-zero total charge: 2.000000 72: Total charge should normally be an integer. See 72: https://manual.gromacs.org/current/user-guide/floating-point.html 72: for discussion on how close it should be to an integer. 72: 72: 72: 72: 72: NOTE 3 [file lysozyme.top, line 1465]: 72: Zero-step energy minimization will alter the coordinates before 72: calculating the energy. If you just want the energy of a single point, 72: try zero-step MD (with unconstrained_start = yes). To do multiple 72: single-point energy evaluations of different configurations of the same 72: topology, use mdrun -rerun. 72: 72: Number of degrees of freedom in T-Coupling group rest is 465.00 72: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.mdp]: 72: You are using a plain Coulomb cut-off, which might produce artifacts. 72: You might want to consider using PME electrostatics. 72: 72: 72: 72: There were 4 NOTEs 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_lysozyme.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 72: Group 0 ( System) has 156 elements 72: Group 1 ( Protein) has 156 elements 72: Group 2 ( Protein-H) has 75 elements 72: Group 3 ( C-alpha) has 10 elements 72: Group 4 ( Backbone) has 30 elements 72: Group 5 ( MainChain) has 40 elements 72: Group 6 ( MainChain+Cb) has 49 elements 72: Group 7 ( MainChain+H) has 52 elements 72: Group 8 ( SideChain) has 104 elements 72: Group 9 ( SideChain-H) has 35 elements 72: Select a group: Will write subset Protein-H of original tpx containing 75 atoms 72: Reduced ilist BONDS from 156 to 75 entries 72: Reduced ilist ANGLES from 281 to 98 entries 72: Reduced ilist PDIHS from 29 to 12 entries 72: Reduced ilist RBDIHS from 313 to 89 entries 72: Reduced ilist LJ14 from 399 to 107 entries 72: Reduced block excls from 156 to 75 index-, 1828 to 635 a-entries 72: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprNoVelocityTest_selectIndexTestWithoutVelocity_extended.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 72: Setting the LD random seed to -134234113 72: 72: Generated 330891 of the 330891 non-bonded parameter combinations 72: 72: Generated 330891 of the 330891 1-4 parameter combinations 72: 72: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 72: Analysing residue names: 72: There are: 10 Protein residues 72: Analysing Protein... 72: 72: This run will generate roughly 0 Mb of data 72: Selected 2: 'Protein-H' 72: [ OK ] ConvertTprNoVelocityTest.selectIndexTestWithoutVelocity (1027 ms) 72: [----------] 1 test from ConvertTprNoVelocityTest (1027 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 2 tests from 2 test suites ran. (2070 ms total) 72: [ PASSED ] 2 tests. 72/103 Test #72: ToolWithLeaksUnitTests .................... Passed 2.10 sec test 73 Start 73: H5mdTests 73: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/h5md-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/H5mdTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/h5md/tests 73: Test timeout computed to be: 30 73: [==========] Running 1 test from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 1 test from H5mdDisabledTest 73: [ RUN ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled 73: [ OK ] H5mdDisabledTest.H5mdThrowsWhenHdf5IsDisabled (0 ms) 73: [----------] 1 test from H5mdDisabledTest (0 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (0 ms total) 73: [ PASSED ] 1 test. 73/103 Test #73: H5mdTests ................................. Passed 0.02 sec test 74 Start 74: FileIOTests 74: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/FileIOTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/fileio/tests 74: Test timeout computed to be: 30 74: [==========] Running 432 tests from 17 test suites. 74: [----------] Global test environment set-up. 74: [----------] 4 tests from Checkpoint 74: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 74: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 74: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 74: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 74: [ RUN ] Checkpoint.KvtRoundTripInt64 74: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 74: [ RUN ] Checkpoint.KvtRoundTripReal 74: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 74: [----------] 4 tests from Checkpoint (0 ms total) 74: 74: [----------] 1 test from StructureIOTest 74: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 74: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (1 ms) 74: [----------] 1 test from StructureIOTest (1 ms total) 74: 74: [----------] 2 tests from FileMD5Test 74: [ RUN ] FileMD5Test.CanComputeMD5 74: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 74: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 74: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 74: [----------] 2 tests from FileMD5Test (1 ms total) 74: 74: [----------] 4 tests from FileTypeTest 74: [ RUN ] FileTypeTest.CorrectValueForEmptyString 74: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 74: [ RUN ] FileTypeTest.CorrectValueForNoExtension 74: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 74: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 74: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 74: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 74: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 74: [----------] 4 tests from FileTypeTest (0 ms total) 74: 74: [----------] 4 tests from ColorMapTest 74: [ RUN ] ColorMapTest.CanReadFromFile 74: [ OK ] ColorMapTest.CanReadFromFile (0 ms) 74: [ RUN ] ColorMapTest.CanWriteToFile 74: [ OK ] ColorMapTest.CanWriteToFile (0 ms) 74: [ RUN ] ColorMapTest.RoundTrip 74: [ OK ] ColorMapTest.RoundTrip (0 ms) 74: [ RUN ] ColorMapTest.SearchWorks 74: [ OK ] ColorMapTest.SearchWorks (0 ms) 74: [----------] 4 tests from ColorMapTest (1 ms total) 74: 74: [----------] 4 tests from MatioTest 74: [ RUN ] MatioTest.CanWriteToFile 74: 33% 66%100%[ OK ] MatioTest.CanWriteToFile (0 ms) 74: [ RUN ] MatioTest.CanConvertToExistingRealMatrix 74: Converted a 4x3 matrix with 4 levels to reals 74: [ OK ] MatioTest.CanConvertToExistingRealMatrix (0 ms) 74: [ RUN ] MatioTest.CanConvertToNewRealMatrix 74: Converted a 4x3 matrix with 4 levels to reals 74: [ OK ] MatioTest.CanConvertToNewRealMatrix (0 ms) 74: [ RUN ] MatioTest.CanReadSingleMatrixAfterWriting 74: 33% 66%100% 33% 66%100%[ OK ] MatioTest.CanReadSingleMatrixAfterWriting (39 ms) 74: [----------] 4 tests from MatioTest (39 ms total) 74: 74: [----------] 3 tests from MrcSerializer 74: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 74: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 74: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 74: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 74: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 74: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 74: [----------] 3 tests from MrcSerializer (0 ms total) 74: 74: [----------] 4 tests from MrcDensityMap 74: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 74: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 74: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 74: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 74: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 74: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 74: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 74: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms) 74: [----------] 4 tests from MrcDensityMap (2 ms total) 74: 74: [----------] 8 tests from MrcDensityMapHeaderTest 74: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 74: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 74: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 74: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 74: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 74: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 74: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 74: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 74: [ RUN ] MrcDensityMapHeaderTest.IsSane 74: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 74: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 74: 74: [----------] 10 tests from ReadTest 74: [ RUN ] ReadTest.get_eint_ReadsInteger 74: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 74: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 74: 74: ERROR 1 [file unknown]: 74: Right hand side '0.8' for parameter 'test' in parameter file is not an 74: integer value 74: 74: 74: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 74: [ RUN ] ReadTest.get_eint_WarnsAboutString 74: 74: ERROR 1 [file unknown]: 74: Right hand side 'hello' for parameter 'test' in parameter file is not an 74: integer value 74: 74: 74: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 74: [ RUN ] ReadTest.get_eint64_ReadsInteger 74: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 74: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 74: 74: ERROR 1 [file unknown]: 74: Right hand side '0.8' for parameter 'test' in parameter file is not an 74: integer value 74: 74: 74: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 74: [ RUN ] ReadTest.get_eint64_WarnsAboutString 74: 74: ERROR 1 [file unknown]: 74: Right hand side 'hello' for parameter 'test' in parameter file is not an 74: integer value 74: 74: 74: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 74: [ RUN ] ReadTest.get_ereal_ReadsInteger 74: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 74: [ RUN ] ReadTest.get_ereal_ReadsFloat 74: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 74: [ RUN ] ReadTest.get_ereal_WarnsAboutString 74: 74: ERROR 1 [file unknown]: 74: Right hand side 'hello' for parameter 'test' in parameter file is not a 74: real value 74: 74: 74: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 74: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 74: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 74: [----------] 10 tests from ReadTest (0 ms total) 74: 74: [----------] 3 tests from TimeControlTest 74: [ RUN ] TimeControlTest.UnSetHasNoValue 74: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 74: [ RUN ] TimeControlTest.CanSetValue 74: [ OK ] TimeControlTest.CanSetValue (0 ms) 74: [ RUN ] TimeControlTest.CanUnsetValueAgain 74: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 74: [----------] 3 tests from TimeControlTest (0 ms total) 74: 74: [----------] 1 test from TngTest 74: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 74: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 74: [----------] 1 test from TngTest (0 ms total) 74: 74: [----------] 4 tests from XvgioTest 74: [ RUN ] XvgioTest.readXvgIntWorks 74: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 74: [ RUN ] XvgioTest.readXvgRealWorks 74: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 74: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 74: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 74: [ RUN ] XvgioTest.readXvgDeprecatedWorks 74: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 74: [----------] 4 tests from XvgioTest (1 ms total) 74: 74: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 74: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 74: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 74: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 74: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 74: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 74: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 74: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 74: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 74: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (2 ms total) 74: 74: [----------] 370 tests from FileTypeMatch/FileTypeTest 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 74: [ RUN ] 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FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/180 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/181 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/182 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/183 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/184 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 74: [ RUN ] 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FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 74: [ RUN ] 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FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 74: [ RUN ] 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FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/180 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/181 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/182 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/183 (0 ms) 74: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 74: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/184 (0 ms) 74: [----------] 370 tests from FileTypeMatch/FileTypeTest (4 ms total) 74: 74: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest 74: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 74: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/0 (0 ms) 74: [ RUN ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 74: [ OK ] InDifferentPrecisionModes/XdrSerializerTest.Works/1 (0 ms) 74: [----------] 2 tests from InDifferentPrecisionModes/XdrSerializerTest (0 ms total) 74: 74: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 74: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 74: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 74: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 74: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 74: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 74: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 74: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 74: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 74: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (2 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 432 tests from 17 test suites ran. (59 ms total) 74: [ PASSED ] 432 tests. 74/103 Test #74: FileIOTests ............................... Passed 0.11 sec test 75 Start 75: SelectionUnitTests 75: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/gromacs/selection/tests 75: Test timeout computed to be: 30 75: [==========] Running 202 tests from 11 test suites. 75: [----------] Global test environment set-up. 75: [----------] 1 test from IndexGroupTest 75: [ RUN ] IndexGroupTest.RemovesDuplicates 75: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 75: [----------] 1 test from IndexGroupTest (0 ms total) 75: 75: [----------] 15 tests from IndexBlockTest 75: [ RUN ] IndexBlockTest.CreatesUnknownBlock 75: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 75: [ RUN ] IndexBlockTest.CreatesAtomBlock 75: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 75: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 75: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 75: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 75: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 75: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 75: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 75: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 75: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 75: [ RUN ] IndexBlockTest.CreatesSingleBlock 75: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 75: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 75: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 75: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 75: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 75: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 75: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 75: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 75: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 75: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 75: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 75: [----------] 15 tests from IndexBlockTest (3 ms total) 75: 75: [----------] 11 tests from IndexMapTest 75: [ RUN ] IndexMapTest.InitializesAtomBlock 75: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 75: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 75: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 75: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 75: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 75: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 75: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 75: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 75: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 75: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 75: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 75: [ RUN ] IndexMapTest.InitializesMoleculeBlock 75: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 75: [ RUN ] IndexMapTest.MapsSingleBlock 75: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 75: [ RUN ] IndexMapTest.MapsResidueBlocks 75: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 75: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 75: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 75: [ RUN ] IndexMapTest.HandlesMultipleRequests 75: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 75: [----------] 11 tests from IndexMapTest (5 ms total) 75: 75: [----------] 3 tests from IndexGroupsAndNamesTest 75: [ RUN ] IndexGroupsAndNamesTest.containsNames 75: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 75: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 75: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 75: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 75: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 75: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 75: 75: [----------] 15 tests from NeighborhoodSearchTest 75: [ RUN ] NeighborhoodSearchTest.SimpleSearch 75: [ OK ] NeighborhoodSearchTest.SimpleSearch (30 ms) 75: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 75: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (31 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearchBox 75: [ OK ] NeighborhoodSearchTest.GridSearchBox (4 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 75: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (11 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 75: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (7 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 75: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (2 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 75: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (4 ms) 75: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 75: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 75: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (61 ms) 75: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 75: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 75: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 75: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 75: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 75: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 75: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 75: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 75: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 75: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (7 ms) 75: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 75: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 75: [----------] 15 tests from NeighborhoodSearchTest (164 ms total) 75: 75: [----------] 13 tests from PositionCalculationTest 75: [ RUN ] PositionCalculationTest.ComputesAtomPositions 75: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 75: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 75: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 75: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 75: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 75: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 75: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 75: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 75: [ RUN ] PositionCalculationTest.ComputesPositionMask 75: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 75: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 75: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (36 ms) 75: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 75: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 75: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 75: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 75: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 75: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 75: [----------] 13 tests from PositionCalculationTest (41 ms total) 75: 75: [----------] 33 tests from SelectionCollectionTest 75: [ RUN ] SelectionCollectionTest.HandlesNoSelections 75: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 75: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 75: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 75: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 75: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 75: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 75: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 75: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms) 75: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 75: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 75: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 75: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 75: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 75: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 75: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 75: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 75: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms) 75: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 75: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 75: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 75: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 75: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 75: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 75: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 75: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 75: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 75: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 75: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 75: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 75: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 75: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 75: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 75: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 75: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 75: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 75: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 75: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 75: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 75: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 75: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 75: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 75: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (1 ms) 75: [----------] 33 tests from SelectionCollectionTest (26 ms total) 75: 75: [----------] 14 tests from SelectionCollectionInteractiveTest 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 75: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 75: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 75: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 75: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 75: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 75: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 75: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 75: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 75: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 75: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 75: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 75: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 75: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 75: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 75: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 75: [----------] 14 tests from SelectionCollectionInteractiveTest (14 ms total) 75: 75: [----------] 71 tests from SelectionCollectionDataTest 75: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 75: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 75: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesResnr 75: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 75: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 75: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 75: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 75: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 75: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesChain 75: [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesMass 75: [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesCharge 75: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 75: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 75: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 75: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesBeta 75: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesResname 75: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 75: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 75: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 75: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 75: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (2 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 75: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 75: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 75: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 75: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (4 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 75: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (3 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 75: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (2 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 75: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (3 ms) 75: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 75: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (2 ms) 75: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 75: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 75: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 75: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 75: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 75: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 75: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (2 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 75: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 75: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 75: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 75: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 75: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 75: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 75: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 75: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 75: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 75: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 75: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 75: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 75: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 75: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 75: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 75: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 75: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsVariableInArithmetic 75: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsVariableInArithmetic (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 75: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (2 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 75: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (2 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 75: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 75: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 75: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 75: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 75: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 75: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 75: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 75: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 75: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (1 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 75: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 75: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 75: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 75: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 75: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 75: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 75: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (3 ms) 75: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 75: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (3 ms) 75: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 75: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (2 ms) 75: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 75: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (3 ms) 75: [----------] 71 tests from SelectionCollectionDataTest (117 ms total) 75: 75: [----------] 17 tests from SelectionOptionTest 75: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 75: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 75: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 75: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 75: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 75: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 75: [ RUN ] SelectionOptionTest.ChecksEmptySelections 75: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 75: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 75: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesTooManySelections 75: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 75: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 75: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesAdjuster 75: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 75: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 75: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 75: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 75: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 75: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 75: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 75: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 75: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 75: [----------] 17 tests from SelectionOptionTest (10 ms total) 75: 75: [----------] 9 tests from SelectionFileOptionTest 75: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 75: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 75: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 75: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 75: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 75: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 75: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 75: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 75: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 75: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 75: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 75: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 75: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 75: [----------] 9 tests from SelectionFileOptionTest (6 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 202 tests from 11 test suites ran. (390 ms total) 75: [ PASSED ] 202 tests. 75/103 Test #75: SelectionUnitTests ........................ Passed 0.43 sec test 76 Start 76: MdrunOutputTests 76: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 12 tests from 5 test suites. 76: [----------] Global test environment set-up. 76: [----------] 1 test from MdrunTest 76: [ RUN ] MdrunTest.WritesHelp 76: [ OK ] MdrunTest.WritesHelp (20 ms) 76: [----------] 1 test from MdrunTest (20 ms total) 76: 76: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 76: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 2573.591 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 1 steps, 0.0 ps. 76: Setting the LD random seed to -164114451 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.074 0.037 199.5 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 4.677 5.131 18.473 0.000 76: Reading frame 0 time 0.000 76: # Atoms 6 76: Reading frame 1 time 0.001 Last frame 1 time 0.001 76: 76: 76: Item #frames Timestep (ps) 76: Step 2 0.001 76: Time 2 0.001 76: Lambda 0 76: Coords 2 0.001 76: Velocities 0 76: Forces 0 76: Box 2 0.001 76: Checking file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 76: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (52 ms) 76: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 2573.591 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 1 steps, 0.0 ps. 76: Setting the LD random seed to -545325121 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.035 0.018 199.1 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 9.740 2.464 8.870 0.001 76: Reading frame 0 time 0.000 76: # Atoms 6 76: Reading frame 1 time 0.001 Last frame 1 time 0.001 76: 76: 76: Item #frames Timestep (ps) 76: Step 2 0.001 76: Time 2 0.001 76: Lambda 0 76: Coords 2 0.001 76: Velocities 0 76: Forces 0 76: Box 2 0.001 76: Checking file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 76: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (30 ms) 76: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group rest is 9.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 76: NVE simulation: will use the initial temperature of 2573.591 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 1 steps, 0.0 ps. 76: Setting the LD random seed to 1584651763 76: 76: Generated 3 of the 3 non-bonded parameter combinations 76: 76: Generated 3 of the 3 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.028 0.014 198.9 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 12.240 1.961 7.059 0.001 76: Reading frame 0 time 0.000 76: # Atoms 3 76: Reading frame 1 time 0.001 Last frame 1 time 0.001 76: 76: 76: Item #frames Timestep (ps) 76: Step 2 0.001 76: Time 2 0.001 76: Lambda 0 76: Coords 2 0.001 76: Velocities 0 76: Forces 0 76: Box 2 0.001 76: Checking file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 76: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (27 ms) 76: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (110 ms total) 76: 76: [----------] 2 tests from Argon12/OutputFiles 76: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Number of degrees of freedom in T-Coupling group System is 33.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 68.810 K for 76: determining the Verlet buffer size 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Argon' 76: 16 steps, 0.0 ps. 76: Generated 1 of the 1 non-bonded parameter combinations 76: 76: Excluding 1 bonded neighbours molecule type 'Argon' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.074 0.037 199.6 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 39.397 0.609 2.193 0.005 76: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (50 ms) 76: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Number of degrees of freedom in T-Coupling group System is 33.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 68.810 K for 76: determining the Verlet buffer size 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'Argon' 76: 16 steps, 0.0 ps. 76: Generated 1 of the 1 non-bonded parameter combinations 76: 76: Excluding 1 bonded neighbours molecule type 'Argon' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.075 0.037 199.8 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 39.263 0.611 2.201 0.005 76: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (54 ms) 76: [----------] 2 tests from Argon12/OutputFiles (104 ms total) 76: 76: [----------] 3 tests from MdrunCanWrite/Trajectories 76: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 6 steps, 0.0 ps. 76: Setting the LD random seed to -613417692 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.068 0.034 199.5 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 17.634 1.361 4.900 0.001 76: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (52 ms) 76: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 6 steps, 0.0 ps. 76: Setting the LD random seed to -474039895 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.063 0.032 199.5 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 19.052 1.260 4.535 0.001 76: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (48 ms) 76: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 6 steps, 0.0 ps. 76: Setting the LD random seed to -1749550087 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.060 0.030 199.4 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 20.152 1.191 4.287 0.001 76: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (46 ms) 76: [----------] 3 tests from MdrunCanWrite/Trajectories (146 ms total) 76: 76: [----------] 3 tests from MdrunCanWrite/NptTrajectories 76: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 2 steps, 0.0 ps. 76: Setting the LD random seed to -1619036233 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.069 0.034 199.5 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 7.516 3.193 11.496 0.001 76: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (50 ms) 76: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 76: The Berendsen barostat does not generate any strictly correct ensemble, 76: and should not be used for new production simulations (in our opinion). 76: We recommend using the C-rescale barostat instead. 76: 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: 76: There was 1 WARNING 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 2 steps, 0.0 ps. 76: Setting the LD random seed to -1880585 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.060 0.030 199.4 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 8.621 2.784 10.022 0.001 76: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (46 ms) 76: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 76: Number of degrees of freedom in T-Coupling group System is 12.00 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There was 1 NOTE 76: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 76: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 76: 76: Using 1 MPI thread 76: Using 2 OpenMP threads 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 2 steps, 0.0 ps. 76: Setting the LD random seed to 452980735 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.056 0.028 199.4 76: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 76: Performance: 9.224 2.602 9.367 0.001 76: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (44 ms) 76: [----------] 3 tests from MdrunCanWrite/NptTrajectories (141 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 12 tests from 5 test suites ran. (584 ms total) 76: [ PASSED ] 12 tests. 76/103 Test #76: MdrunOutputTests .......................... Passed 0.61 sec test 77 Start 77: MdrunModulesTests 77: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 15 tests from 3 test suites. 77: [----------] Global test environment set-up. 77: [----------] 9 tests from DensityFittingTest 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 2 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 3 steps. 77: Potential Energy = -3.85652608067156e+03 77: Maximum force = 4.50998690851897e+03 on atom 3 77: Norm of force = 1.68168494163492e+03 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -137401386 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (15 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 2 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 3 steps. 77: Potential Energy = -9.82077921283928e+03 77: Maximum force = 7.39548334240075e+03 on atom 2 77: Norm of force = 2.78250777177324e+03 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -581061637 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (15 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 77: 77: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (12 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Overriding nsteps with value passed on the command line: 4 steps 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 4 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 5 steps. 77: Potential Energy = -5.47393359520241e+03 77: Maximum force = 6.13219949575544e+03 on atom 2 77: Norm of force = 1.77021426574818e+03 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -576098401 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (14 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 77: 77: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (11 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 2 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 3 steps. 77: Potential Energy = -3.85652608067156e+03 77: Maximum force = 4.50998690851897e+03 on atom 3 77: Norm of force = 1.68168494163492e+03 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 402489334 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (13 ms) 77: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 2 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 3 steps. 77: Potential Energy = -2.71386626041483e+04 77: Maximum force = 6.78276506555709e+03 on atom 2 77: Norm of force = 1.96088641457984e+03 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1339263859 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (13 ms) 77: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 77: 77: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1104:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 77: Setting the LD random seed to 1241513260 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 77: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (13 ms) 77: [ RUN ] DensityFittingTest.CheckpointWorks 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (2) 77: 77: Number of degrees of freedom in T-Coupling group rest is 33.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -1073955129 77: 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.087 0.043 199.6 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 5.977 4.015 14.455 0.001 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 77: Can not increase nstlist because an NVE ensemble is used 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'Argon' 77: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.041 0.021 199.3 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 21.042 1.141 4.106 0.003 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (81 ms) 77: [----------] 9 tests from DensityFittingTest (190 ms total) 77: 77: [----------] 4 tests from MimicTest 77: [ RUN ] MimicTest.OneQuantumMol 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 21.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 77: NVE simulation with an initial temperature of zero: will use a Verlet 77: buffer of 10%. Check your energy drift! 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 77: 77: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 77: Reading frame 0 time 0.000 Last frame 0 time 0.000 77: 77: NOTE: 16 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.000 184.3 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 232.897 0.103 0.371 0.032 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -4966765 77: 77: Generated 10 of the 10 non-bonded parameter combinations 77: 77: Generated 10 of the 10 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] MimicTest.OneQuantumMol (12 ms) 77: [ RUN ] MimicTest.AllQuantumMol 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 21.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 77: NVE simulation with an initial temperature of zero: will use a Verlet 77: buffer of 10%. Check your energy drift! 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 77: 77: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 77: Reading frame 0 time 0.000 Last frame 0 time 0.000 77: 77: NOTE: 15 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.000 184.2 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 261.841 0.092 0.330 0.036 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -423630951 77: 77: Generated 10 of the 10 non-bonded parameter combinations 77: 77: Generated 10 of the 10 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] MimicTest.AllQuantumMol (13 ms) 77: [ RUN ] MimicTest.TwoQuantumMol 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 21.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 77: NVE simulation with an initial temperature of zero: will use a Verlet 77: buffer of 10%. Check your energy drift! 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 77: 77: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 77: Reading frame 0 time 0.000 Last frame 0 time 0.000 77: 77: NOTE: 14 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.000 183.4 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 275.162 0.087 0.314 0.038 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1878360059 77: 77: Generated 10 of the 10 non-bonded parameter combinations 77: 77: Generated 10 of the 10 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] MimicTest.TwoQuantumMol (12 ms) 77: [ RUN ] MimicTest.BondCuts 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group rest is 66.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 77: NVE simulation: will use the initial temperature of 300.368 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 77: 77: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 77: Reading frame 0 time 0.000 Last frame 0 time 0.000 77: 77: NOTE: 13 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 189.1 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 131.300 0.183 0.658 0.035 77: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -269396014 77: 77: Generated 2211 of the 2211 non-bonded parameter combinations 77: 77: Generated 2211 of the 2211 1-4 parameter combinations 77: 77: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] MimicTest.BondCuts (34 ms) 77: [----------] 4 tests from MimicTest (72 ms total) 77: 77: [----------] 2 tests from WithIntegrator/ImdTest 77: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 77: Generating 1-4 interactions: fudge = 1 77: 77: NOTE 1 [file glycine_vacuo.top, line 12]: 77: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 77: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 77: the time step of 2.0e-03 ps. 77: Maybe you forgot to change the constraints mdp option. 77: 77: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 77: 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: IMD: Enabled. This simulation will accept incoming IMD connections. 77: IMD: Pulling from IMD remote is enabled (-imdpull). 77: IMD: Setting port for connection requests to 0. 77: IMD: Setting up incoming socket. 77: IMD: Listening for IMD connection on port 43431. 77: IMD: -imdwait not set, starting simulation. 77: starting mdrun 'Glycine' 77: 2 steps, 0.0 ps. 77: Setting the LD random seed to -54804515 77: 77: Generated 20503 of the 20503 non-bonded parameter combinations 77: 77: Generated 17396 of the 20503 1-4 parameter combinations 77: 77: Excluding 3 bonded neighbours molecule type 'Glycine' 77: 77: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/glycine_vacuo.gro', all velocities are zero 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.097 0.048 199.6 77: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 77: Performance: 10.704 2.242 16.144 0.001 77: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (263 ms) 77: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 77: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 77: apply to steep. 77: 77: Generating 1-4 interactions: fudge = 1 77: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 2 NOTEs 77: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 77: Using 1 MPI thread 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: 77: IMD: Enabled. This simulation will accept incoming IMD connections. 77: IMD: Pulling from IMD remote is enabled (-imdpull). 77: IMD: Setting port for connection requests to 0. 77: IMD: Setting up incoming socket. 77: IMD: Listening for IMD connection on port 42599. 77: IMD: -imdwait not set, starting simulation. 77: 77: Steepest Descents: 77: Tolerance (Fmax) = 1.00000e+01 77: Number of steps = 2 77: 77: Energy minimization reached the maximum number of steps before the forces 77: reached the requested precision Fmax < 10. 77: 77: writing lowest energy coordinates. 77: 77: Steepest Descents did not converge to Fmax < 10 in 3 steps. 77: Potential Energy = 1.19770464690297e+03 77: Maximum force = 1.77948604657896e+04 on atom 9 77: Norm of force = 7.87328617833980e+03 77: Setting the LD random seed to -72590625 77: 77: Generated 20503 of the 20503 non-bonded parameter combinations 77: 77: Generated 17396 of the 20503 1-4 parameter combinations 77: 77: Excluding 3 bonded neighbours molecule type 'Glycine' 77: 77: This run will generate roughly 0 Mb of data 77: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (212 ms) 77: [----------] 2 tests from WithIntegrator/ImdTest (476 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 15 tests from 3 test suites ran. (787 ms total) 77: [ PASSED ] 15 tests. 77/103 Test #77: MdrunModulesTests ......................... Passed 0.81 sec test 78 Start 78: MdrunIOTests 78: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 76 tests from 13 test suites. 78: [----------] Global test environment set-up. 78: [----------] 9 tests from GromppTest 78: [ RUN ] GromppTest.EmptyMdpFileWorks 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to 1339022847 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.EmptyMdpFileWorks (10 ms) 78: [ RUN ] GromppTest.SimulatedAnnealingWorks 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Simulated annealing for group rest: Periodic, 4 timepoints 78: Time (ps) Temperature (K) 78: 0.0 298.0 78: 2.0 320.0 78: 4.0 320.0 78: 6.0 298.0 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -654843905 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.SimulatedAnnealingWorks (8 ms) 78: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Simulated annealing for group Methanol: Single, 3 timepoints 78: Time (ps) Temperature (K) 78: 0.0 298.0 78: 3.0 280.0 78: 6.0- 270.0 78: Simulated annealing for group SOL: Periodic, 4 timepoints 78: Time (ps) Temperature (K) 78: 0.0 298.0 78: 2.0 320.0 78: 4.0 320.0 78: 6.0 298.0 78: Number of degrees of freedom in T-Coupling group Methanol is 7.20 78: Number of degrees of freedom in T-Coupling group SOL is 4.80 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -34873377 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (8 ms) 78: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 78: Setting the LD random seed to 2142672078 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (14 ms) 78: [ RUN ] GromppTest.HandlesMaxwarn 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Number of degrees of freedom in T-Coupling group System is 12.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: There was 1 WARNING 78: Setting the LD random seed to -88350737 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.HandlesMaxwarn (8 ms) 78: [ RUN ] GromppTest.MaxwarnShouldBePositive 78: [ OK ] GromppTest.MaxwarnShouldBePositive (1 ms) 78: [ RUN ] GromppTest.ValidTransformationCoord 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Pull group 1 'SOL' has 3 atoms 78: Pull group 2 'Methanol' has 3 atoms 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 5 78: 2 3 2 0.613 nm 0.000 nm 78: 0.613 nm 0.000 nm 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -1203 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] GromppTest.ValidTransformationCoord (10 ms) 78: [ RUN ] GromppTest.InvalidTransformationCoord 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Pull group 1 'SOL' has 3 atoms 78: Pull group 2 'Methanol' has 3 atoms 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 5 78: 2 3 2 0.613 nm 0.000 nm 78: Setting the LD random seed to -874512609 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: [ OK ] GromppTest.InvalidTransformationCoord (10 ms) 78: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 78: Setting the LD random seed to -1949435913 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (12 ms) 78: [----------] 9 tests from GromppTest (85 ms total) 78: 78: [----------] 6 tests from MdrunTerminationTest 78: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -1666197123 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.077 0.039 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 6.686 3.590 12.923 0.000 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Setting nsteps to 4 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 2 78: Runtime for the run 0.002 ps 78: Run end step 2 78: Run end time 0.002 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.036 0.018 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.159 1.695 6.102 0.001 78: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (78 ms) 78: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 1, rlist from 1.032 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 100 steps, 0.1 ps. 78: 78: Step 4: Run time exceeded 0.000 hours, will terminate the run within 200 steps 78: Setting the LD random seed to -80085281 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.063 0.032 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 275.559 0.087 0.314 0.019 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Setting nsteps to 102 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 100 78: Runtime for the run 0.1 ps 78: Run end step 100 78: Run end time 0.1 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 102 78: Runtime for the run 0.102 ps 78: Run end step 102 78: Run end time 0.102 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.036 0.018 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.290 1.679 6.046 0.001 78: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (68 ms) 78: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -137452737 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.058 0.029 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 8.879 2.703 9.731 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Setting nsteps to 4 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 2 78: Runtime for the run 0.002 ps 78: Run end step 2 78: Run end time 0.002 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.053 0.026 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 9.830 2.442 8.790 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Setting nsteps to 6 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 6 78: Runtime for the run 0.006 ps 78: Run end step 6 78: Run end time 0.006 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.050 0.025 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 10.302 2.330 8.386 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Setting nsteps to 8 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 6 78: Runtime for the run 0.006 ps 78: Run end step 6 78: Run end time 0.006 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 8 78: Runtime for the run 0.008 ps 78: Run end step 8 78: Run end time 0.008 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.048 0.024 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 10.700 2.243 8.075 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: NOTE: 14 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.001 0.000 177.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 289.910 0.083 0.298 0.020 78: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (144 ms) 78: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to 2046271359 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.054 0.027 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 9.627 2.493 8.975 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Setting nsteps to 4 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 4 steps, 0.0 ps. 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 2 78: Runtime for the run 0.002 ps 78: Run end step 2 78: Run end time 0.002 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.056 0.028 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 15.356 1.563 5.626 0.001 78: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (78 ms) 78: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to -270143619 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.050 0.025 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 10.401 2.307 8.307 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Setting nsteps to 4 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 2 78: Runtime for the run 0.002 ps 78: Run end step 2 78: Run end time 0.002 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (40 ms) 78: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 2 steps, 0.0 ps. 78: Setting the LD random seed to 1261796217 78: 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.056 0.028 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 9.206 2.607 9.386 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Setting nsteps to 4 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 78: Input file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 2 78: Runtime for the run 0.002 ps 78: Run end step 2 78: Run end time 0.002 ps 78: 78: 78: Output file: 78: Run start step 0 78: Run start time 0 ps 78: Step to be made during run 4 78: Runtime for the run 0.004 ps 78: Run end step 4 78: Run end time 0.004 ps 78: 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.048 0.024 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 10.746 2.233 8.040 0.001 78: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (72 ms) 78: [----------] 6 tests from MdrunTerminationTest (482 ms total) 78: 78: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 78: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.070 0.035 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 41.742 0.575 2.070 0.003 78: trr version: GMX_trn_file (double precision) 78: 78: 78: Will write trr: Trajectory in portable xdr format 78: Last frame -1 time 0.016 78: -> frame 0 time 0.016 78: Last written: frame 0 time 0.016 78: 78: 78: Will write trr: Trajectory in portable xdr format 78: Last frame -1 time 0.016 78: 78: Dumping frame at t= 0.016 ps 78: -> frame 0 time 0.016 78: Last written: frame 0 time 0.016 78: 78: 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_output.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Last frame -1 time 0.016 78: 78: There were 3 NOTEs 78: Note that major changes are planned in future for trjconv, to improve usability and utility. 78: Note that major changes are planned in future for trjconv, to improve usability and utility. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: Analysing residue names: 78: There are: 2 Water residues 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: Reading Coordinates, Velocities and Box size from old trajectory 78: 78: Will read whole trajectory 78: 78: Using frame at t = 0.016 ps 78: 78: Starting time for run is 0 ps 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (61 ms) 78: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.071 0.036 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 41.233 0.582 2.095 0.003 78: 78: 78: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (48 ms) 78: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (110 ms total) 78: 78: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.060 0.030 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.204 0.488 1.756 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.072 0.036 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.427 1.120 4.032 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.072 0.036 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.650 1.109 3.991 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (132 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.068 0.034 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 42.806 0.561 2.018 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.096 0.048 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 16.126 1.488 5.358 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.068 0.034 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 22.781 1.054 3.793 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (146 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.068 0.034 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 43.116 0.557 2.004 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.073 0.036 199.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.333 1.125 4.050 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.089 0.045 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.390 1.380 4.968 0.002 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (146 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.080 0.040 199.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 36.748 0.653 2.351 0.005 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.069 0.035 199.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 22.463 1.068 3.846 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.096 0.048 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 16.191 1.482 5.336 0.002 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (152 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.078 0.039 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 37.805 0.635 2.285 0.005 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.074 0.037 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.015 1.142 4.111 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.088 0.044 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.689 1.357 4.884 0.002 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (149 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.083 0.041 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 35.466 0.677 2.436 0.005 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.072 0.036 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.669 1.108 3.987 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.073 0.037 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.286 1.127 4.059 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (147 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.192 0.096 199.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 15.267 1.572 5.659 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.074 0.037 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 20.852 1.151 4.143 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.074 0.037 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.067 1.139 4.101 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (202 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.077 0.039 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 38.064 0.631 2.270 0.005 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.073 0.037 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.161 1.134 4.083 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.099 0.049 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 15.725 1.526 5.494 0.002 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (155 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.097 0.048 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 30.316 0.792 2.850 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.089 0.044 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.515 1.370 4.933 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.092 0.046 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 16.858 1.424 5.125 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (169 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.064 0.032 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.609 0.526 1.894 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.071 0.035 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.960 1.093 3.934 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.089 0.045 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.365 1.382 4.976 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (142 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.070 0.035 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 42.092 0.570 2.053 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.071 0.036 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.743 1.104 3.974 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.086 0.043 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 18.150 1.322 4.760 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (144 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.082 0.041 199.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 35.773 0.671 2.415 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.084 0.042 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 18.427 1.302 4.689 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.073 0.037 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.178 1.133 4.080 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (151 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.064 0.032 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.805 0.524 1.886 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.071 0.035 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.944 1.094 3.937 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.085 0.043 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 18.176 1.320 4.753 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (148 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.080 0.040 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 36.488 0.658 2.368 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.080 0.040 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 19.321 1.242 4.472 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.081 0.041 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 19.119 1.255 4.519 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (162 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.080 0.040 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 36.520 0.657 2.366 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.071 0.036 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.840 1.099 3.956 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.073 0.036 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.322 1.126 4.052 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (163 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.075 0.038 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 39.144 0.613 2.207 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.075 0.037 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 20.769 1.156 4.160 0.001 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.071 0.036 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 21.894 1.096 3.946 0.002 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (145 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.090 0.045 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 32.544 0.737 2.655 0.011 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.082 0.041 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 18.983 1.264 4.551 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.084 0.042 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 18.431 1.302 4.688 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (213 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.091 0.046 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 32.264 0.744 2.678 0.011 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.083 0.042 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 18.705 1.283 4.619 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.090 0.045 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.308 1.387 4.992 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (211 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.093 0.047 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 31.370 0.765 2.754 0.011 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.087 0.043 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.880 1.342 4.832 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.084 0.042 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 18.507 1.297 4.669 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (212 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: NVE simulation: will use the initial temperature of 456.887 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 5 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.097 0.048 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 30.371 0.790 2.845 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.079 0.040 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 19.600 1.224 4.408 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.083 0.041 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 18.751 1.280 4.608 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (208 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.091 0.046 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 32.162 0.746 2.686 0.011 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.090 0.045 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.256 1.391 5.007 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.097 0.049 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 15.953 1.504 5.416 0.005 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (302 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.099 0.049 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 29.697 0.808 2.909 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.091 0.045 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.106 1.403 5.051 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.088 0.044 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.564 1.366 4.919 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (575 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.096 0.048 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 30.649 0.783 2.819 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.091 0.046 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.044 1.408 5.069 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.088 0.044 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.602 1.364 4.909 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (284 ms) 78: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: NOTE 2 [file unknown]: 78: You are using constraints on all bonds, whereas the forcefield has been 78: parametrized only with constraints involving hydrogen atoms. We suggest 78: using constraints = h-bonds instead, this will also improve performance. 78: 78: Number of degrees of freedom in T-Coupling group System is 23.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: There are 9 non-linear virtual site constructions. Their contribution to 78: the energy error is approximated. In most cases this does not affect the 78: error significantly. 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 78: 78: turning all bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 78: 78: Cleaning up constraints and constant bonded interactions with virtual sites 78: 78: Removed 18 Angles with virtual sites, 21 left 78: 78: Removed 10 Proper Dih.s with virtual sites, 44 left 78: 78: Converted 15 Constraints with virtual sites to connections, 7 left 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.096 0.048 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 30.391 0.790 2.843 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.098 0.049 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 15.902 1.509 5.433 0.005 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 78: 78: Update groups can not be used for this system because an incompatible virtual site type is used 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine dipeptide in vacuo' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.091 0.046 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 17.009 1.411 5.080 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (363 ms) 78: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (4833 ms total) 78: 78: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.123 0.062 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 23.761 1.010 3.636 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.105 0.053 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.740 1.628 5.862 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.111 0.056 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 13.948 1.721 6.194 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (250 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.122 0.061 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 24.019 0.999 3.597 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.106 0.053 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.631 1.640 5.905 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.112 0.056 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 13.855 1.732 6.236 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (248 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.126 0.063 199.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 23.307 1.030 3.707 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.103 0.052 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 15.085 1.591 5.728 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.115 0.058 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 13.464 1.783 6.417 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (251 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: NVE simulation: will use the initial temperature of 294.908 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 294.908 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.133 0.066 199.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 22.134 1.084 3.904 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.139 0.069 199.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 11.196 2.144 7.717 0.005 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.113 0.057 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 13.703 1.751 6.305 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (271 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.126 0.063 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 23.252 1.032 3.716 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.110 0.055 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.144 1.697 6.109 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.105 0.053 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.719 1.631 5.870 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (312 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.126 0.063 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 23.318 1.029 3.705 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.259 0.130 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 5.996 4.002 14.409 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.117 0.059 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 13.236 1.813 6.527 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (738 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.143 0.071 199.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 20.547 1.168 4.205 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.110 0.055 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.109 1.701 6.124 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.118 0.059 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 13.183 1.820 6.554 0.005 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (311 ms) 78: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.128 0.064 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 22.957 1.045 3.764 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 20, rlist from 0.749 to 0.842 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.106 0.053 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.662 1.637 5.893 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.252 0.126 199.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 6.177 3.885 13.987 0.003 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (387 ms) 78: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2773 ms total) 78: 78: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.016 0.008 197.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 186.849 0.128 0.462 0.026 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.011 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 68.354 0.351 1.264 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.024 0.012 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 64.752 0.371 1.334 0.009 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (62 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.019 0.010 198.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 149.740 0.160 0.577 0.021 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.014 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 54.203 0.443 1.594 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 58.868 0.408 1.468 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (68 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 91.841 0.261 0.941 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.024 0.012 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 65.240 0.368 1.324 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.653 0.526 1.893 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (75 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.021 0.010 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 140.112 0.171 0.617 0.019 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.028 0.014 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 55.083 0.436 1.569 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.025 0.012 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 62.968 0.381 1.372 0.009 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (68 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.037 0.019 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 79.271 0.303 1.090 0.011 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.031 0.016 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 49.528 0.485 1.744 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.028 0.014 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 54.795 0.438 1.577 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (79 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.043 0.022 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 67.444 0.356 1.281 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.013 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 57.823 0.415 1.494 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.011 198.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 68.109 0.352 1.269 0.009 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (78 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.033 0.017 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 87.732 0.274 0.985 0.012 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 48.323 0.497 1.788 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.024 0.012 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 64.794 0.370 1.333 0.009 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (76 ms) 78: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.040 0.020 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 73.724 0.326 1.172 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.035 0.018 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 44.234 0.543 1.953 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.033 0.016 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 47.150 0.509 1.832 0.007 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (85 ms) 78: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (594 ms total) 78: 78: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 78: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.014 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 106.511 0.225 0.811 0.015 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.012 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 66.353 0.362 1.302 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.012 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 67.062 0.358 1.288 0.009 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (68 ms) 78: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.892 0.446 200.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 3.292 7.290 26.243 0.000 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.022 0.011 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 69.916 0.343 1.236 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.026 0.013 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 60.378 0.397 1.431 0.008 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (501 ms) 78: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (569 ms total) 78: 78: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.051 0.026 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 57.541 0.417 1.502 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.013 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 57.681 0.416 1.498 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.029 0.015 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 52.626 0.456 1.642 0.007 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (85 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 90.215 0.266 0.958 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.012 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 67.103 0.358 1.288 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.012 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 67.110 0.358 1.287 0.009 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (70 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.020 0.010 198.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 143.340 0.167 0.603 0.020 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.677 0.525 1.892 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.037 0.019 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 41.432 0.579 2.085 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (77 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 78: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 78: 1 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.042 0.021 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 70.453 0.341 1.226 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 48.524 0.495 1.781 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.035 0.018 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 43.823 0.548 1.972 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (85 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.043 0.022 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 68.117 0.352 1.268 0.009 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.032 0.016 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 48.670 0.493 1.775 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.023 0.012 198.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 67.488 0.356 1.280 0.009 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (80 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.033 0.016 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 89.115 0.269 0.970 0.012 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.027 0.014 194.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 56.189 0.427 1.538 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 198.9 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.714 0.525 1.890 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (80 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 78: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 78: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.035 0.017 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 84.259 0.285 1.025 0.012 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 199.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.104 0.532 1.916 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.033 0.017 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 46.633 0.515 1.853 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (83 ms) 78: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (564 ms total) 78: 78: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 78: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: MTTK coupling is deprecated and will soon be removed 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: MTTK coupling is deprecated and will soon be removed 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.040 0.020 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 72.645 0.330 1.189 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.036 0.018 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 42.554 0.564 2.030 0.006 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.034 0.017 198.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 45.580 0.527 1.896 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (89 ms) 78: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (89 ms total) 78: 78: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 78: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'FirstWaterMolecule' has 3 atoms 78: Pull group 2 'SecondWaterMolecule' has 3 atoms 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 2 78: 2 3 5 1.112 nm 1.000 nm 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'FirstWaterMolecule' has 3 atoms 78: Pull group 2 'SecondWaterMolecule' has 3 atoms 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 2 78: 2 3 5 1.112 nm 1.000 nm 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.071 0.036 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 41.033 0.585 2.106 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.053 0.027 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 29.155 0.823 2.963 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.054 0.027 199.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 28.583 0.840 3.023 0.002 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (127 ms) 78: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'FirstWaterMolecule' has 3 atoms 78: Pull group 2 'SecondWaterMolecule' has 3 atoms 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 2 78: 2 3 5 1.112 nm 1.000 nm 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'FirstWaterMolecule' has 3 atoms 78: Pull group 2 'SecondWaterMolecule' has 3 atoms 78: Number of degrees of freedom in T-Coupling group System is 9.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 2573.591 K for 78: determining the Verlet buffer size 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 3 2 78: 2 3 5 1.112 nm 1.000 nm 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps. 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 3 of the 3 non-bonded parameter combinations 78: 78: Generated 3 of the 3 1-4 parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: NOTE: 14 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.071 0.036 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 41.270 0.582 2.094 0.003 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.059 0.030 199.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 26.276 0.913 3.288 0.002 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc2' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.046 0.023 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 33.692 0.712 2.564 0.002 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (126 ms) 78: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (253 ms total) 78: 78: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 78: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: Setting the AWH bias MC random seed to -2097282 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'C_&_r_1' has 1 atoms 78: Pull group 2 'N_&_r_2' has 1 atoms 78: Pull group 3 'CA' has 1 atoms 78: Pull group 4 'C_&_r_2' has 1 atoms 78: Pull group 5 'N_&_r_3' has 1 atoms 78: Number of degrees of freedom in T-Coupling group System is 51.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 1 0 78: 2 1 0 179.098 deg 0.000 deg 78: 2 1 0 78: 3 1 0 158.667 deg 0.000 deg 78: 78: There were 2 NOTEs 78: Setting the AWH bias MC random seed to -3195546 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'C_&_r_1' has 1 atoms 78: Pull group 2 'N_&_r_2' has 1 atoms 78: Pull group 3 'CA' has 1 atoms 78: Pull group 4 'C_&_r_2' has 1 atoms 78: Pull group 5 'N_&_r_3' has 1 atoms 78: Number of degrees of freedom in T-Coupling group System is 51.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 1 0 78: 2 1 0 179.098 deg 0.000 deg 78: 2 1 0 78: 3 1 0 158.667 deg 0.000 deg 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.078 0.039 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 37.707 0.636 2.291 0.010 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.056 0.028 198.3 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 27.779 0.864 3.110 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.057 0.029 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 26.967 0.890 3.204 0.007 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (205 ms) 78: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 78: Setting the AWH bias MC random seed to -11148697 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'C_&_r_1' has 1 atoms 78: Pull group 2 'N_&_r_2' has 1 atoms 78: Pull group 3 'CA' has 1 atoms 78: Pull group 4 'C_&_r_2' has 1 atoms 78: Pull group 5 'N_&_r_3' has 1 atoms 78: Number of degrees of freedom in T-Coupling group System is 51.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 1 0 78: 2 1 0 179.098 deg 0.000 deg 78: 2 1 0 78: 3 1 0 158.667 deg 0.000 deg 78: 78: There were 2 NOTEs 78: Setting the AWH bias MC random seed to -1426727173 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Pull group 1 'C_&_r_1' has 1 atoms 78: Pull group 2 'N_&_r_2' has 1 atoms 78: Pull group 3 'CA' has 1 atoms 78: Pull group 4 'C_&_r_2' has 1 atoms 78: Pull group 5 'N_&_r_3' has 1 atoms 78: Number of degrees of freedom in T-Coupling group System is 51.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: Pull group natoms pbc atom distance at start reference at t=0 78: 1 1 0 78: 2 1 0 179.098 deg 0.000 deg 78: 2 1 0 78: 3 1 0 158.667 deg 0.000 deg 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 16 steps, 0.0 ps. 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2145 of the 2145 non-bonded parameter combinations 78: 78: Generated 2145 of the 2145 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.055 0.028 198.7 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 52.587 0.456 1.643 0.013 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.057 0.029 198.2 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 26.956 0.890 3.205 0.007 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Alanine-dipeptide' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.061 0.030 198.8 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 25.518 0.941 3.386 0.006 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (193 ms) 78: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (399 ms total) 78: 78: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 78: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 79.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There was 1 NOTE 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps. 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: Generated 2485 of the 2485 non-bonded parameter combinations 78: 78: Generated 2485 of the 2485 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'nonanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.068 0.034 199.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 43.183 0.556 2.001 0.018 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 8 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: NOTE: 14 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.080 0.040 199.5 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 19.383 1.238 4.458 0.008 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun '30 atom system in water' 78: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.055 0.028 198.4 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 28.095 0.854 3.075 0.012 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (228 ms) 78: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (228 ms total) 78: 78: [----------] 3 tests from Checking/InitialConstraintsTest 78: [ RUN ] Checking/InitialConstraintsTest.Works/0 78: Number of degrees of freedom in T-Coupling group rest is 11.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 1141.954 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 1 steps, 0.0 ps. 78: Setting the LD random seed to -154047237 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.043 0.022 199.1 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 7.926 3.028 10.901 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (36 ms) 78: [ RUN ] Checking/InitialConstraintsTest.Works/1 78: Number of degrees of freedom in T-Coupling group rest is 11.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 78: NVE simulation: will use the initial temperature of 1141.954 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 2 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 1 steps, 0.0 ps. 78: Setting the LD random seed to -1245980762 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.025 0.012 199.0 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.029 1.711 6.158 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (26 ms) 78: [ RUN ] Checking/InitialConstraintsTest.Works/2 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 78: Integrator method md-vv-avek is implemented primarily for validation 78: purposes; for molecular dynamics, you should probably be using md or 78: md-vv 78: 78: Number of degrees of freedom in T-Coupling group rest is 11.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 78: NVE simulation: will use the initial temperature of 1141.954 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 78: You are using a plain Coulomb cut-off, which might produce artifacts. 78: You might want to consider using PME electrostatics. 78: 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 1 steps, 0.0 ps. 78: Setting the LD random seed to -1141919809 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 78: 78: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.024 0.012 198.6 78: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 78: Performance: 14.413 1.665 5.995 0.001 78: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (25 ms) 78: [----------] 3 tests from Checking/InitialConstraintsTest (88 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 76 tests from 13 test suites ran. (11277 ms total) 78: [ PASSED ] 76 tests. 78/103 Test #78: MdrunIOTests .............................. Passed 11.31 sec test 79 Start 79: MdrunTestsOneRank 79: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" 79: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 31 tests from 9 test suites. 79: [----------] Global test environment set-up. 79: [----------] 2 tests from AwhTest 79: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (10) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 20 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.184 0.093 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 19.606 1.224 4.407 0.005 79: [ OK ] AwhTest.SingleBiasMultiDimCanRun (147 ms) 79: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (10) 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'C_&_r_1' has 1 atoms 79: Pull group 2 'N_&_r_2' has 1 atoms 79: Pull group 3 'CA' has 1 atoms 79: Pull group 4 'C_&_r_2' has 1 atoms 79: Pull group 5 'N_&_r_3' has 1 atoms 79: Number of degrees of freedom in T-Coupling group System is 51.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 1 0 79: 2 1 0 179.098 deg 0.000 deg 79: 2 1 0 79: 3 1 0 158.667 deg 0.000 deg 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 20 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.019 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 95.234 0.252 0.907 0.024 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 196.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 168.266 0.143 0.513 0.043 79: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (99 ms) 79: [----------] 2 tests from AwhTest (247 ms total) 79: 79: [----------] 1 test from CompelTest 79: [ RUN ] CompelTest.SwapCanRun 79: Generating 1-4 interactions: fudge = 0.5 79: Split0 group 'Ch0' contains 83 atoms. 79: Split1 group 'Ch1' contains 83 atoms. 79: Solvent group 'SOL' contains 11931 atoms. 79: Swap group 'NA+' contains 19 atoms. 79: Swap group 'CL-' contains 19 atoms. 79: Number of degrees of freedom in T-Coupling group System is 27869.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 79: Removing center of mass motion in the presence of position restraints 79: might cause artifacts. When you are using position restraints to 79: equilibrate a macro-molecule, the artifacts are usually negligible. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Update groups can not be used for this system because there are three or more consecutively coupled constraints 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: SWAP: Determining initial numbers of ions per compartment. 79: SWAP: Setting pointers for checkpoint writing 79: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 79: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 79: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 79: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 79: starting mdrun 'Channel_coco in octane membrane' 79: 2 steps, 0.0 ps. 79: Setting the LD random seed to -1141000653 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein' 79: 79: turning all bonds into constraints... 79: 79: Excluding 3 bonded neighbours molecule type 'OCT' 79: 79: turning all bonds into constraints... 79: 79: Excluding 1 bonded neighbours molecule type 'NA' 79: 79: turning all bonds into constraints... 79: 79: Excluding 1 bonded neighbours molecule type 'CL' 79: 79: turning all bonds into constraints... 79: 79: Excluding 3 bonded neighbours molecule type 'Protein' 79: 79: Excluding 3 bonded neighbours molecule type 'OCT' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning all bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 79: 79: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 1 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 10 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 1.316 0.658 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 1.575 15.236 219.394 0.063 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 79: 79: Update groups can not be used for this system because there are three or more consecutively coupled constraints 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: SWAP: Setting pointers for checkpoint writing 79: SWAP: Copying channel fluxes from checkpoint file data 79: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 79: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 79: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 79: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 79: starting mdrun 'Channel_coco in octane membrane' 79: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 1.140 0.570 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 1.819 13.192 189.969 0.073 79: [ OK ] CompelTest.SwapCanRun (2549 ms) 79: [----------] 1 test from CompelTest (2549 ms total) 79: 79: [----------] 6 tests from BondedInteractionsTest 79: [ RUN ] BondedInteractionsTest.NormalBondWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 2 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 17 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 184.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 237.320 0.101 0.364 0.011 79: Setting the LD random seed to -608370713 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.NormalBondWorks (13 ms) 79: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 2 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 16 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 183.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 279.620 0.086 0.309 0.013 79: Setting the LD random seed to -1346527265 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.TabulatedBondWorks (13 ms) 79: [ RUN ] BondedInteractionsTest.NormalAngleWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 4 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 14 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 183.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 293.907 0.082 0.294 0.014 79: Setting the LD random seed to -37770597 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.NormalAngleWorks (11 ms) 79: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 4 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 15 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 183.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 300.987 0.080 0.287 0.014 79: Setting the LD random seed to -278201617 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (12 ms) 79: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 4 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 14 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 183.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 293.907 0.082 0.294 0.014 79: Setting the LD random seed to -1074308225 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.NormalDihedralWorks (11 ms) 79: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: 79: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 79: In moleculetype 'butane' 4 atoms are not bound by a potential or 79: constraint to any other atom in the same moleculetype. Although 79: technically this might not cause issues in a simulation, this often means 79: that the user forgot to add a bond/potential/constraint or put multiple 79: molecules in the same moleculetype definition by mistake. Run with -v to 79: get information for each atom. 79: 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 79: NVE simulation with an initial temperature of zero: will use a Verlet 79: buffer of 10%. Check your energy drift! 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 79: 79: Reading frames from gro file 'A single butane', 4 atoms. 79: Reading frame 0 time 0.000 Last frame 0 time 0.000 79: 79: NOTE: 11 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.000 187.1 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 211.675 0.113 0.408 0.010 79: Setting the LD random seed to -1434521673 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'butane' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (13 ms) 79: [----------] 6 tests from BondedInteractionsTest (77 ms total) 79: 79: [----------] 2 tests from BoxDeformationTest 79: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (10) 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 79: For a correct single-point energy evaluation with nsteps = 0, use 79: continuation = yes to avoid constraining the input coordinates. 79: 79: Number of degrees of freedom in T-Coupling group rest is 33.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Argon' 79: 0 steps, 0.0 ps. 79: 79: NOTE: 20 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.000 0.000 156.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 562.714 0.043 0.307 0.039 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2138767317 79: 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Setting gen_seed to 1979531155 79: 79: Velocities were taken from a Maxwell distribution at 0 K 79: 79: This run will generate roughly 0 Mb of data 79: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (13 ms) 79: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (10) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group rest is 1293.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Setting the LD random seed to 1878439886 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 79: 79: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 79: 79: Estimate for the relative computational load of the PME mesh part: 0.09 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.370 0.185 199.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 19.603 1.224 8.815 0.074 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (1256 ms) 79: [----------] 2 tests from BoxDeformationTest (1271 ms total) 79: 79: [----------] 1 test from PositionRestraintCommTest 79: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 79: You have set rlist larger than the interaction cut-off, but you also have 79: verlet-buffer-tolerance > 0. Will set rlist using 79: verlet-buffer-tolerance. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (10) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 79: 13489 atoms are not part of any of the VCM groups 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 79: 13489 atoms are not part of any center of mass motion removal group. 79: This may lead to artifacts. 79: In most cases one should use one group for the whole system. 79: 79: Number of degrees of freedom in T-Coupling group System is 29527.73 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 79: Removing center of mass motion in the presence of position restraints 79: might cause artifacts. When you are using position restraints to 79: equilibrate a macro-molecule, the artifacts are usually negligible. 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Channel_coco in octane membrane' 79: 10 steps, 0.0 ps. 79: Setting the LD random seed to -554795171 79: 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein' 79: 79: Excluding 3 bonded neighbours molecule type 'OCT' 79: 79: Excluding 1 bonded neighbours molecule type 'NA' 79: 79: Excluding 1 bonded neighbours molecule type 'CL' 79: 79: Excluding 3 bonded neighbours molecule type 'Protein' 79: 79: Excluding 3 bonded neighbours molecule type 'OCT' 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/OctaneSandwich.gro' 79: 79: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: Chain0: 2.207 2.168 7.330 79: Chain1: 2.228 2.186 2.401 79: Chain0: 2.207 2.168 7.330 79: Chain1: 2.228 2.186 2.401 79: 79: This run will generate roughly 1 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 2.234 1.117 200.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 1.701 14.106 101.565 0.136 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (2350 ms) 79: [----------] 1 test from PositionRestraintCommTest (2350 ms total) 79: 79: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 79: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 3 [file ala.top, line 256]: 79: For energy conservation with LINCS, lincs_iter should be 2 or larger. 79: 79: 79: Number of degrees of freedom in T-Coupling group rest is 54.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'UNNAMED in water' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to -59810409 79: 79: Generated 2211 of the 2211 non-bonded parameter combinations 79: 79: Generated 2211 of the 2211 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 79: 79: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 79: 79: Estimate for the relative computational load of the PME mesh part: 0.93 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.158 0.079 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 5.463 4.393 15.816 0.001 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 3 [file ala.top, line 256]: 79: For energy conservation with LINCS, lincs_iter should be 2 or larger. 79: 79: 79: Number of degrees of freedom in T-Coupling group rest is 54.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'UNNAMED in water' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to 795565757 79: 79: Generated 2211 of the 2211 non-bonded parameter combinations 79: 79: Generated 2211 of the 2211 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 79: 79: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 79: 79: Estimate for the relative computational load of the PME mesh part: 0.93 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.019 0.010 197.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 45.302 0.530 1.907 0.012 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 79: 79: 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (178 ms) 79: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 3 [file ala.top, line 256]: 79: For energy conservation with LINCS, lincs_iter should be 2 or larger. 79: 79: 79: Number of degrees of freedom in T-Coupling group rest is 54.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'UNNAMED in water' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to 801111991 79: 79: Generated 2211 of the 2211 non-bonded parameter combinations 79: 79: Generated 2211 of the 2211 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 79: 79: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 79: 79: Estimate for the relative computational load of the PME mesh part: 0.93 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 197.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 40.525 0.592 2.132 0.011 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 3 [file ala.top, line 256]: 79: For energy conservation with LINCS, lincs_iter should be 2 or larger. 79: 79: 79: Number of degrees of freedom in T-Coupling group rest is 54.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 79: The optimal PME mesh load for parallel simulations is below 0.5 79: and for highly parallel simulations between 0.25 and 0.33, 79: for higher performance, increase the cut-off and the PME grid spacing. 79: 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'UNNAMED in water' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to -546455553 79: 79: Generated 2211 of the 2211 non-bonded parameter combinations 79: 79: Generated 2211 of the 2211 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 79: 79: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 79: Calculating fourier grid dimensions for X Y Z 79: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 79: 79: Estimate for the relative computational load of the PME mesh part: 0.93 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.043 0.022 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 19.912 1.205 4.339 0.005 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 79: 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (106 ms) 79: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (285 ms total) 79: 79: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 79: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to -750784523 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.065 0.033 199.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 13.231 1.814 6.530 0.001 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'FirstWaterMolecule' has 3 atoms 79: Pull group 2 'SecondWaterMolecule' has 3 atoms 79: Number of degrees of freedom in T-Coupling group rest is 9.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 1.112 nm 1.000 nm 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 4 steps, 0.0 ps. 79: Setting the LD random seed to -9471587 79: 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.053 0.027 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 16.249 1.477 5.317 0.001 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 79: 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (91 ms) 79: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (91 ms total) 79: 79: [----------] 12 tests from FreezeWorks/FreezeGroupTest 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 246.451 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.051 0.026 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 30.246 0.793 2.857 0.008 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (59 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 246.451 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.040 0.020 198.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 38.491 0.624 2.245 0.010 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (52 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 246.451 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.044 0.022 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 34.784 0.690 2.484 0.009 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (55 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 246.451 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.074 0.037 199.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 20.954 1.145 4.123 0.005 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (69 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 79: NVE simulation: will use the initial temperature of 246.451 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 4 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.047 0.024 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 32.597 0.736 2.651 0.008 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (56 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 79: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 79: Parrinello-Rahman is not implemented in md-vv. 79: 79: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 17 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.049 0.025 199.2 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 31.720 0.757 2.724 0.008 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (76 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.045 0.023 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 34.474 0.696 2.506 0.009 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (67 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.042 0.021 198.9 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 36.459 0.658 2.370 0.009 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (65 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.167 0.084 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.282 2.586 9.308 0.002 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (195 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.168 0.084 199.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.266 2.590 9.324 0.002 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (194 ms) 79: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 79: There are 5 atoms that are fully frozen and part of COMM removal 79: group(s), removing these atoms from the COMM removal group(s) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 79: There are 3 atoms that are frozen along less then 3 dimensions and part 79: of COMM removal group(s), due to limitations in the code these still 79: contribute to the mass of the COM along frozen dimensions and therefore 79: the COMM correction will be too small. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 79: You are using a plain Coulomb cut-off, which might produce artifacts. 79: You might want to consider using PME electrostatics. 79: 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 79: 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'Alanine-dipeptide' 79: 8 steps, 0.0 ps. 79: Generated 2145 of the 2145 non-bonded parameter combinations 79: 79: Generated 2145 of the 2145 1-4 parameter combinations 79: 79: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 79: 79: turning H bonds into constraints... 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.163 0.081 199.8 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 9.542 2.515 9.054 0.002 79: 79: 79: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (193 ms) 79: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1088 ms total) 79: 79: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 79: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 79: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: Net Acceleration in X direction, will not be corrected 79: Net Acceleration in Y direction, will not be corrected 79: Net Acceleration in Z direction, will not be corrected 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to 1324875593 79: 79: Velocities were taken from a Maxwell distribution at 0 K 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.023 0.012 198.5 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 134.475 0.178 1.285 0.005 79: 79: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (26 ms) 79: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 79: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 79: Net Acceleration in X direction, will not be corrected 79: Net Acceleration in Y direction, will not be corrected 79: Net Acceleration in Z direction, will not be corrected 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because verlet-buffer-tolerance is not set or used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -1494768153 79: 79: Velocities were taken from a Maxwell distribution at 0 K 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.011 198.4 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 144.493 0.166 1.196 0.005 79: 79: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (25 ms) 79: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 79: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 79: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 79: Net Acceleration in X direction, will not be corrected 79: Net Acceleration in Y direction, will not be corrected 79: Net Acceleration in Z direction, will not be corrected 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to 1425989435 79: 79: Velocities were taken from a Maxwell distribution at 0 K 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.024 0.012 198.7 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 126.304 0.190 1.368 0.004 79: 79: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (25 ms) 79: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 79: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 79: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 79: on the accuracy of your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 79: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 79: < 0 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Generating 1-4 interactions: fudge = 0.5 79: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 79: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 79: Net Acceleration in X direction, will not be corrected 79: Net Acceleration in Y direction, will not be corrected 79: Net Acceleration in Z direction, will not be corrected 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 79: Can not increase nstlist because verlet-buffer-tolerance is not set or used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 8 steps, 0.0 ps. 79: Generated 3 of the 3 non-bonded parameter combinations 79: 79: Generated 3 of the 3 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Setting gen_seed to -143949969 79: 79: Velocities were taken from a Maxwell distribution at 0 K 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.032 0.016 199.0 79: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 79: Performance: 97.781 0.245 1.767 0.003 79: 79: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (29 ms) 79: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (107 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 31 tests from 9 test suites ran. (8209 ms total) 79: [ PASSED ] 30 tests. 79: [ SKIPPED ] 1 test, listed below: 79: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 79/103 Test #79: MdrunTestsOneRank ......................... Passed 8.25 sec test 80 Start 80: MdrunTestsTwoRanks 80: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" 80: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 31 tests from 9 test suites. 80: [----------] Global test environment set-up. 80: [----------] 2 tests from AwhTest 80: [ RUN ] AwhTest.SingleBiasMultiDimCanRun 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_SingleBiasMultiDimCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 2 MPI threads 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 15.2%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 7.6%. 80: 80: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 47 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.324 0.082 396.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 22.206 1.081 3.891 0.006 80: [ OK ] AwhTest.SingleBiasMultiDimCanRun (139 ms) 80: [ RUN ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'C_&_r_1' has 1 atoms 80: Pull group 2 'N_&_r_2' has 1 atoms 80: Pull group 3 'CA' has 1 atoms 80: Pull group 4 'C_&_r_2' has 1 atoms 80: Pull group 5 'N_&_r_3' has 1 atoms 80: Number of degrees of freedom in T-Coupling group System is 51.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 1 0 80: 2 1 0 179.098 deg 0.000 deg 80: 2 1 0 80: 3 1 0 158.667 deg 0.000 deg 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 20 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 31.5%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 13.6%. 80: 80: NOTE: 13.6 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 16 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 5.474 1.384 395.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.311 18.306 65.901 0.000 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AwhTest_MultiBiasCanRunAndRestartFromCheckpoint.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Overriding nsteps with value passed on the command line: 20 steps, 0.02 ps 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 40 steps, 0.0 ps (continuing from step 20, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 26.8%. 80: The balanceable part of the MD step is 48%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 13.0%. 80: 80: NOTE: 13.0 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 17 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 5.225 1.317 396.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.378 17.420 62.712 0.000 80: [ OK ] AwhTest.MultiBiasCanRunAndRestartFromCheckpoint (4139 ms) 80: [----------] 2 tests from AwhTest (4279 ms total) 80: 80: [----------] 1 test from CompelTest 80: [ RUN ] CompelTest.SwapCanRun 80: Generating 1-4 interactions: fudge = 0.5 80: Split0 group 'Ch0' contains 83 atoms. 80: Split1 group 'Ch1' contains 83 atoms. 80: Solvent group 'SOL' contains 11931 atoms. 80: Swap group 'NA+' contains 19 atoms. 80: Swap group 'CL-' contains 19 atoms. 80: Number of degrees of freedom in T-Coupling group System is 27869.00 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: SWAP: Determining initial numbers of ions per compartment. 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 2 steps, 0.0 ps. 80: Setting the LD random seed to -169902470 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: turning all bonds into constraints... 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: turning all bonds into constraints... 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning all bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/OctaneSandwich-z.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 80: 80: Calculated rlist for 1x1 atom pair-list as 1.256 nm, buffer size 0.256 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 1.211 nm, buffer size 0.211 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.9%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 23 % of the run time was spent in domain decomposition, 80: 6 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 7.344 1.852 396.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.560 42.868 617.304 0.022 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Overriding nsteps with value passed on the command line: 2 steps, 0.008 ps 80: 80: Update groups can not be used for this system because there are three or more consecutively coupled constraints 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: SWAP: Setting pointers for checkpoint writing 80: SWAP: Copying channel fluxes from checkpoint file data 80: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 80: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 80: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 80: starting mdrun 'Channel_coco in octane membrane' 80: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 5.096 1.290 395.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.804 29.860 429.986 0.032 80: [ OK ] CompelTest.SwapCanRun (6153 ms) 80: [----------] 1 test from CompelTest (6154 ms total) 80: 80: [----------] 6 tests from BondedInteractionsTest 80: [ RUN ] BondedInteractionsTest.NormalBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 77 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.969 0.254 381.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.340 70.617 254.221 0.000 80: Setting the LD random seed to -1342251345 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalBondWorks (842 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 2 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 80 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.937 0.246 380.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.351 68.394 246.219 0.000 80: Setting the LD random seed to -958660930 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedBondWorks (807 ms) 80: [ RUN ] BondedInteractionsTest.NormalAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 80 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.921 0.242 380.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.357 67.285 242.227 0.000 80: Setting the LD random seed to -1250181156 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalAngleWorks (827 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 79 % of the run time was spent in domain decomposition, 80: 4 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.937 0.246 380.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.351 68.395 246.223 0.000 80: Setting the LD random seed to -889522690 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (839 ms) 80: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 81 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.954 0.251 380.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.345 69.602 250.567 0.000 80: Setting the LD random seed to 1069217594 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.NormalDihedralWorks (843 ms) 80: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: 80: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 80: In moleculetype 'butane' 4 atoms are not bound by a potential or 80: constraint to any other atom in the same moleculetype. Although 80: technically this might not cause issues in a simulation, this often means 80: that the user forgot to add a bond/potential/constraint or put multiple 80: molecules in the same moleculetype definition by mistake. Run with -v to 80: get information for each atom. 80: 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 80: NVE simulation with an initial temperature of zero: will use a Verlet 80: buffer of 10%. Check your energy drift! 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro' 80: 80: Reading frames from gro file 'A single butane', 4 atoms. 80: Reading frame 0 time 0.000 Last frame 0 time 0.000 80: 80: NOTE: 70 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.050 0.275 382.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.315 76.268 274.565 0.000 80: Setting the LD random seed to 1794505643 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'butane' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/butane1.gro', all velocities are zero 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (855 ms) 80: [----------] 6 tests from BondedInteractionsTest (5018 ms total) 80: 80: [----------] 2 tests from BoxDeformationTest 80: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 80: For a correct single-point energy evaluation with nsteps = 0, use 80: continuation = yes to avoid constraining the input coordinates. 80: 80: Number of degrees of freedom in T-Coupling group rest is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Argon' 80: 0 steps, 0.0 ps. 80: 80: NOTE: 47 % of the run time was spent in domain decomposition, 80: 9 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 23 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.354 0.104 340.7 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.662 14.438 103.953 0.000 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1539274975 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Setting gen_seed to -16812617 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (720 ms) 80: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group rest is 1293.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 20 steps, 0.0 ps. 80: Setting the LD random seed to -1417674755 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 80: 80: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 80: 80: Estimate for the relative computational load of the PME mesh part: 0.09 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB got disabled because it was unsuitable to use. 80: Average load imbalance: 31.4%. 80: The balanceable part of the MD step is 14%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 4.5%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 11.808 2.968 397.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.223 19.629 141.330 0.005 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (4684 ms) 80: [----------] 2 tests from BoxDeformationTest (5405 ms total) 80: 80: [----------] 1 test from PositionRestraintCommTest 80: [ RUN ] PositionRestraintCommTest.PositionRestraintsTwoCOMs 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: You have set rlist larger than the interaction cut-off, but you also have 80: verlet-buffer-tolerance > 0. Will set rlist using 80: verlet-buffer-tolerance. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (10) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any of the VCM groups 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: 13489 atoms are not part of any center of mass motion removal group. 80: This may lead to artifacts. 80: In most cases one should use one group for the whole system. 80: 80: Number of degrees of freedom in T-Coupling group System is 29527.73 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs_input.mdp]: 80: Removing center of mass motion in the presence of position restraints 80: might cause artifacts. When you are using position restraints to 80: equilibrate a macro-molecule, the artifacts are usually negligible. 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Changing nstlist from 10 to 20, rlist from 0.965 to 1.066 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Channel_coco in octane membrane' 80: 10 steps, 0.0 ps. 80: Setting the LD random seed to -272927818 80: 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 1 bonded neighbours molecule type 'NA' 80: 80: Excluding 1 bonded neighbours molecule type 'CL' 80: 80: Excluding 3 bonded neighbours molecule type 'Protein' 80: 80: Excluding 3 bonded neighbours molecule type 'OCT' 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/OctaneSandwich.gro' 80: 80: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.990 nm, buffer size 0.090 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.965 nm, buffer size 0.065 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: Chain0: 2.207 2.168 7.330 80: Chain1: 2.228 2.186 2.401 80: 80: This run will generate roughly 1 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 8.407 2.118 397.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.898 26.737 192.508 0.072 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PositionRestraintCommTest_PositionRestraintsTwoCOMs.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Last energy frame read 1 time 0.020 [ OK ] PositionRestraintCommTest.PositionRestraintsTwoCOMs (3984 ms) 80: [----------] 1 test from PositionRestraintCommTest (3985 ms total) 80: 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -512762439 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.93 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 10 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 8 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.352 0.604 389.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.715 33.551 120.785 0.000 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -1143310340 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.93 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 15 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 10 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.032 0.524 387.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.825 29.107 104.785 0.000 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 80: 80: 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (2585 ms) 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 2096609241 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.93 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 14 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 8 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.336 0.600 389.4 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.720 33.329 119.985 0.000 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file ala.top, line 256]: 80: For energy conservation with LINCS, lincs_iter should be 2 or larger. 80: 80: 80: Number of degrees of freedom in T-Coupling group rest is 54.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 80: The optimal PME mesh load for parallel simulations is below 0.5 80: and for highly parallel simulations between 0.25 and 0.33, 80: for higher performance, increase the cut-off and the PME grid spacing. 80: 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'UNNAMED in water' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to -46139931 80: 80: Generated 2211 of the 2211 non-bonded parameter combinations 80: 80: Generated 2211 of the 2211 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 80: 80: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 80: Calculating fourier grid dimensions for X Y Z 80: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 80: 80: Estimate for the relative computational load of the PME mesh part: 0.93 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 15 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 12 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.064 0.532 388.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 0.812 29.551 106.385 0.000 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (2606 ms) 80: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (5192 ms total) 80: 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 80: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 1073610734 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 12 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.632 0.424 384.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.019 23.553 84.790 0.000 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group rest is 9.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 4 steps, 0.0 ps. 80: Setting the LD random seed to 1843002878 80: 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 12 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.632 0.424 384.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.019 23.553 84.790 0.000 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 80: 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (2129 ms) 80: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (2129 ms total) 80: 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 43.4%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 16.9%. 80: 80: NOTE: 16.9 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 19 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 14 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.129 0.548 388.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.419 16.911 60.881 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (1161 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 36.6%. 80: The balanceable part of the MD step is 42%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 15.3%. 80: 80: NOTE: 15.3 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 20 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 13 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.115 0.544 388.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.430 16.788 60.436 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (1200 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 45.3%. 80: The balanceable part of the MD step is 38%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 17.0%. 80: 80: NOTE: 17.0 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 19 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 14 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.161 0.556 388.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.399 17.158 61.770 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (1203 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 22.4%. 80: The balanceable part of the MD step is 46%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 10.3%. 80: 80: NOTE: 10.3 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 17 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 22 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.368 0.608 389.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.279 18.763 67.547 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (1256 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: NVE simulation: will use the initial temperature of 246.451 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 246.451 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.755 nm, buffer size 0.055 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 21.0%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 10.6%. 80: 80: NOTE: 10.6 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 17 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.673 0.684 390.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.137 21.109 75.994 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (1339 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80: ./src/programs/mdrun/tests/freezegroups.cpp:209: Skipped 80: Parrinello-Rahman is not implemented in md-vv. 80: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 13 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.810 0.468 386.8 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.662 14.442 51.992 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (1131 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 15 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.987 0.512 388.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.519 15.800 56.881 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (1175 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vacuo.gro' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 14 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.761 0.460 382.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.691 14.196 51.104 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (1115 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in domain decomposition, 80: 1 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 17 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.761 0.456 386.3 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.706 14.072 50.658 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (1279 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 15 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.843 0.476 387.2 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.634 14.689 52.881 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (1276 ms) 80: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 5 atoms that are fully frozen and part of COMM removal 80: group(s), removing these atoms from the COMM removal group(s) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: There are 3 atoms that are frozen along less then 3 dimensions and part 80: of COMM removal group(s), due to limitations in the code these still 80: contribute to the mass of the COM along frozen dimensions and therefore 80: the COMM correction will be too small. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 80: 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'Alanine-dipeptide' 80: 8 steps, 0.0 ps. 80: Generated 2145 of the 2145 non-bonded parameter combinations 80: 80: Generated 2145 of the 2145 1-4 parameter combinations 80: 80: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 80: 80: turning H bonds into constraints... 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 15 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.729 0.448 386.1 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 1.736 13.825 49.770 0.000 80: 80: 80: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (1255 ms) 80: [----------] 12 tests from FreezeWorks/FreezeGroupTest (13397 ms total) 80: 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 1398630911 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 6.7%. 80: The balanceable part of the MD step is 36%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.4%. 80: 80: 80: NOTE: 16 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 14 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.048 0.528 387.9 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 2.946 8.147 58.661 0.000 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (1111 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 1941176187 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 14.5%. 80: The balanceable part of the MD step is 35%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 5.1%. 80: 80: NOTE: 5.1 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 80: You can also consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 20 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 14 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.176 0.560 388.6 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 2.777 8.641 62.217 0.000 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (1139 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to -689665 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.4%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.3%. 80: 80: 80: NOTE: 18 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 22 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.303 0.592 389.0 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 2.627 9.136 65.776 0.000 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (1160 ms) 80: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: With Verlet lists and no buffer tolerance, the optimal nstlist is >= 10, 80: with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect 80: on the accuracy of your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 80: < 0 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 80: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 80: Net Acceleration in X direction, will not be corrected 80: Net Acceleration in Y direction, will not be corrected 80: Net Acceleration in Z direction, will not be corrected 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 80: Can not increase nstlist because verlet-buffer-tolerance is not set or used 80: Using 2 MPI threads 80: 80: Non-default thread affinity set, disabling internal thread affinity 80: 80: Using 2 OpenMP threads per tMPI thread 80: 80: starting mdrun 'spc2' 80: 8 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Setting gen_seed to 2147407199 80: 80: Velocities were taken from a Maxwell distribution at 0 K 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 6.0%. 80: The balanceable part of the MD step is 38%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.3%. 80: 80: 80: NOTE: 19 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 23 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.424 0.624 388.5 80: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 80: Performance: 2.492 9.629 69.332 0.000 80: 80: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (1208 ms) 80: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (4620 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 31 tests from 9 test suites ran. (50323 ms total) 80: [ PASSED ] 30 tests. 80: [ SKIPPED ] 1 test, listed below: 80: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 80/103 Test #80: MdrunTestsTwoRanks ........................ Passed 50.36 sec test 81 Start 81: MdrunSingleRankAlgorithmsTests 81: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 5 tests from 3 test suites. 81: [----------] Global test environment set-up. 81: [----------] 1 test from DispersionCorrectionTest 81: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 30.00 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 81: There are 9 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 81: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 81: 81: Update groups can not be used for this system because an incompatible virtual site type is used 81: 81: Using 1 MPI thread 81: Using 2 OpenMP threads 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Alanine dipeptide in vacuo' 81: 200 steps, 0.4 ps. 81: Setting the LD random seed to 930869247 81: 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Converted 3 Bonds with virtual sites to connections, 7 left 81: 81: Removed 18 Angles with virtual sites, 21 left 81: 81: Removed 10 Proper Dih.s with virtual sites, 44 left 81: 81: Converted 12 Constraints with virtual sites to connections, 0 left 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.115 0.057 199.6 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 604.195 0.040 0.286 0.101 81: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (147 ms) 81: [----------] 1 test from DispersionCorrectionTest (147 ms total) 81: 81: [----------] 1 test from OriresTest 81: [ RUN ] OriresTest.OriresCanRun 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 518.00 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There was 1 NOTE 81: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 81: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 81: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 81: 81: 81: Using 1 MPI thread 81: Using 2 OpenMP threads 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 81: 10 steps, 0.0 ps. 81: Setting the LD random seed to -117645325 81: 81: Generated 2145 of the 2145 non-bonded parameter combinations 81: 81: Generated 2145 of the 2145 1-4 parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 81: 81: turning H bonds into constraints... 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: turning H bonds into constraints... 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/orires_1lvz.gro' 81: 81: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 81: 81: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.101 0.051 199.5 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 37.400 0.642 4.620 0.047 81: [ OK ] OriresTest.OriresCanRun (1256 ms) 81: [----------] 1 test from OriresTest (1256 ms total) 81: 81: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 81: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 81: Number of degrees of freedom in T-Coupling group rest is 10.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 2 OpenMP threads 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Dipoles' 81: 20 steps, 0.1 ps. 81: Setting the LD random seed to 2113924846 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Dipole' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 81: 81: Searching the wall atom type(s) 81: 81: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.044 0.022 198.9 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 202.807 0.118 1.065 0.004 81: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) 81: 81: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (68 ms) 81: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 81: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 81: The supported numbers are > 1. 81: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 81: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 81: With epsilon_surface > 0 all molecules should be neutral. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 81: With epsilon_surface > 0 you can only use domain decomposition when there 81: are only small molecules with all bonds constrained (mdrun will check for 81: this). 81: 81: Number of degrees of freedom in T-Coupling group rest is 9.00 81: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 81: The optimal PME mesh load for parallel simulations is below 0.5 81: and for highly parallel simulations between 0.25 and 0.33, 81: for higher performance, increase the cut-off and the PME grid spacing. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 2 OpenMP threads 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Dipoles' 81: 20 steps, 0.1 ps. 81: Setting the LD random seed to 2134890093 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Dipole' 81: 81: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/dipoles.gro', all velocities are zero 81: 81: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 81: Calculating fourier grid dimensions for X Y Z 81: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 81: 81: Estimate for the relative computational load of the PME mesh part: 1.00 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.040 0.020 199.2 81: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 81: Performance: 224.200 0.107 0.963 0.004 81: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 81: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (46 ms) 81: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (115 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 5 tests from 3 test suites ran. (1567 ms total) 81: [ PASSED ] 5 tests. 81/103 Test #81: MdrunSingleRankAlgorithmsTests ............ Passed 1.59 sec test 82 Start 82: Minimize1RankTests 82: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/Minimize1RankTests.xml" 82: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 82: Test timeout computed to be: 600 82: [==========] Running 12 tests from 2 test suites. 82: [----------] Global test environment set-up. 82: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Steepest Descents: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Steepest Descents did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = -4.79910463671072e+01 82: Maximum force = 1.86297359432219e+02 on atom 13 82: Norm of force = 8.77219865482162e+01 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1002 ms) 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Polak-Ribiere Conjugate Gradients: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: F-max = 3.02331e+02 on atom 3 82: F-Norm = 1.18024e+02 82: 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = -5.58622538633294e+01 82: Maximum force = 4.27274822366508e+02 on atom 13 82: Norm of force = 1.84530029253822e+02 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1020 ms) 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 1 82: Number of degrees of freedom in T-Coupling group System is 22.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Steepest Descents: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Steepest Descents did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = 3.19376899751521e+02 82: Maximum force = 9.99884921009767e+03 on atom 9 82: Norm of force = 4.61669565054298e+03 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 82: 82: Generated 17396 of the 20503 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Glycine' 82: 82: turning H bonds into constraints... 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (196 ms) 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 1 82: 82: NOTE 2 [file glycine_vacuo.top, line 12]: 82: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 82: 82: Number of degrees of freedom in T-Coupling group System is 22.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Polak-Ribiere Conjugate Gradients: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: F-max = 2.41575e+04 on atom 10 82: F-Norm = 1.18451e+04 82: 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = 1.51743018140924e+02 82: Maximum force = 7.42089573409110e+03 on atom 9 82: Norm of force = 3.56929298615738e+03 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 82: 82: Generated 17396 of the 20503 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Glycine' 82: 82: turning H bonds into constraints... 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (198 ms) 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: 82: NOTE 2 [file unknown]: 82: You are using constraints on all bonds, whereas the forcefield has been 82: parametrized only with constraints involving hydrogen atoms. We suggest 82: using constraints = h-bonds instead, this will also improve performance. 82: 82: Number of degrees of freedom in T-Coupling group System is 23.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: Update groups can not be used for this system because an incompatible virtual site type is used 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Steepest Descents: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Steepest Descents did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = -1.56984193848276e+02 82: Maximum force = 4.56923624626405e+02 on atom 17 82: Norm of force = 1.83258377168346e+02 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 82: 82: turning all bonds into constraints... 82: 82: Cleaning up constraints and constant bonded interactions with virtual sites 82: 82: Removed 18 Angles with virtual sites, 21 left 82: 82: Removed 10 Proper Dih.s with virtual sites, 44 left 82: 82: Converted 15 Constraints with virtual sites to connections, 7 left 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (31 ms) 82: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: 82: NOTE 2 [file unknown]: 82: You are using constraints on all bonds, whereas the forcefield has been 82: parametrized only with constraints involving hydrogen atoms. We suggest 82: using constraints = h-bonds instead, this will also improve performance. 82: 82: 82: NOTE 3 [file unknown]: 82: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 82: 82: Number of degrees of freedom in T-Coupling group System is 23.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: Update groups can not be used for this system because an incompatible virtual site type is used 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Polak-Ribiere Conjugate Gradients: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: F-max = 1.06800e+03 on atom 28 82: F-Norm = 4.26922e+02 82: 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = -1.69410778678185e+02 82: Maximum force = 2.18225948474010e+02 on atom 17 82: Norm of force = 7.92068036537787e+01 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 82: 82: Generated 2145 of the 2145 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 82: 82: turning all bonds into constraints... 82: 82: Cleaning up constraints and constant bonded interactions with virtual sites 82: 82: Removed 18 Angles with virtual sites, 21 left 82: 82: Removed 10 Proper Dih.s with virtual sites, 44 left 82: 82: Converted 15 Constraints with virtual sites to connections, 7 left 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (31 ms) 82: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2481 ms total) 82: 82: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Steepest Descents: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: 82: writing lowest energy coordinates. 82: 82: Steepest Descents converged to Fmax < 10 in 1 steps 82: Potential Energy = -9.74257075835450e-01 82: Maximum force = 4.01322929015108e+00 on atom 1 82: Norm of force = 1.63839399694368e+00 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (13 ms) 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Polak-Ribiere Conjugate Gradients: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: F-max = 4.01323e+00 on atom 1 82: F-Norm = 1.63839e+00 82: 82: 82: writing lowest energy coordinates. 82: 82: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 82: Potential Energy = -9.90642313893957e-01 82: Maximum force = 2.57812909491105e+00 on atom 1 82: Norm of force = 1.05251679559258e+00 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (13 ms) 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Low-Memory BFGS Minimizer: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: Using 10 BFGS correction steps. 82: 82: F-max = 4.01323e+00 on atom 1 82: F-Norm = 1.63839e+00 82: 82: 82: writing lowest energy coordinates. 82: 82: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 82: Potential Energy = -9.90642313893957e-01 82: Maximum force = 2.57812909491105e+00 on atom 1 82: Norm of force = 1.05251679559258e+00 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (13 ms) 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 1 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Steepest Descents: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Steepest Descents did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = 3.19395484891518e+02 82: Maximum force = 9.97041707197911e+03 on atom 9 82: Norm of force = 4.62274878665467e+03 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 82: 82: Generated 17396 of the 20503 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Glycine' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (198 ms) 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 1 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Polak-Ribiere Conjugate Gradients: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: F-max = 2.41672e+04 on atom 10 82: F-Norm = 1.19357e+04 82: 82: 82: Energy minimization reached the maximum number of steps before the forces 82: reached the requested precision Fmax < 10. 82: 82: writing lowest energy coordinates. 82: 82: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 82: Potential Energy = 1.56258793899479e+02 82: Maximum force = 7.50181017480397e+03 on atom 9 82: Norm of force = 3.61390332564874e+03 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 82: 82: Generated 17396 of the 20503 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Glycine' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (198 ms) 82: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 82: 82: Generating 1-4 interactions: fudge = 1 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 82: COM removal frequency is set to (4). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 82: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 82: 82: Using 1 MPI thread 82: Using 2 OpenMP threads 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: 82: Low-Memory BFGS Minimizer: 82: Tolerance (Fmax) = 1.00000e+01 82: Number of steps = 4 82: Using 10 BFGS correction steps. 82: 82: F-max = 2.41672e+04 on atom 10 82: F-Norm = 1.19357e+04 82: 82: 82: Energy minimization has stopped, but the forces have not converged to the 82: requested precision Fmax < 10 (which may not be possible for your system). It 82: stopped because the algorithm tried to make a new step whose size was too 82: small, or there was no change in the energy since last step. Either way, we 82: regard the minimization as converged to within the available machine 82: precision, given your starting configuration and EM parameters. 82: 82: writing lowest energy coordinates. 82: 82: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 82: but did not reach the requested Fmax < 10. 82: Potential Energy = 5.61116097794204e+02 82: Maximum force = 1.26854826291223e+04 on atom 10 82: Norm of force = 6.06436286976271e+03 82: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 82: 82: Generated 17396 of the 20503 1-4 parameter combinations 82: 82: Excluding 3 bonded neighbours molecule type 'Glycine' 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (198 ms) 82: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (638 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 12 tests from 2 test suites ran. (3151 ms total) 82: [ PASSED ] 12 tests. 82/103 Test #82: Minimize1RankTests ........................ Passed 3.19 sec test 83 Start 83: Minimize2RankTests 83: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/Minimize2RankTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 12 tests from 2 test suites. 83: [----------] Global test environment set-up. 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 83: Using 2 MPI threads 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -4.79910463671071e+01 83: Maximum force = 1.86297359432220e+02 on atom 13 83: Norm of force = 8.77219865482162e+01 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1006 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 3.02331e+02 on atom 3 83: F-Norm = 1.18024e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -5.58622538633295e+01 83: Maximum force = 4.27274822366505e+02 on atom 13 83: Norm of force = 1.84530029253821e+02 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2844 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.19376899751521e+02 83: Maximum force = 9.99884921009767e+03 on atom 9 83: Norm of force = 4.61669565054298e+03 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1388 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: 83: NOTE 2 [file glycine_vacuo.top, line 12]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 22.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41575e+04 on atom 10 83: F-Norm = 1.18451e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.51743018140925e+02 83: Maximum force = 7.42089573409110e+03 on atom 9 83: Norm of force = 3.56929298615738e+03 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: turning H bonds into constraints... 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1947 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.56984193848276e+02 83: Maximum force = 4.56923624626405e+02 on atom 17 83: Norm of force = 1.83258377168346e+02 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (1315 ms) 83: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 2 [file unknown]: 83: You are using constraints on all bonds, whereas the forcefield has been 83: parametrized only with constraints involving hydrogen atoms. We suggest 83: using constraints = h-bonds instead, this will also improve performance. 83: 83: 83: NOTE 3 [file unknown]: 83: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 83: 83: Number of degrees of freedom in T-Coupling group System is 23.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 83: Update groups can not be used for this system because an incompatible virtual site type is used 83: 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 1.06800e+03 on atom 28 83: F-Norm = 4.26922e+02 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = -1.69410778678187e+02 83: Maximum force = 2.18225948474252e+02 on atom 17 83: Norm of force = 7.92068036538114e+01 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 83: 83: Generated 2145 of the 2145 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 83: 83: turning all bonds into constraints... 83: 83: Cleaning up constraints and constant bonded interactions with virtual sites 83: 83: Removed 18 Angles with virtual sites, 21 left 83: 83: Removed 10 Proper Dih.s with virtual sites, 44 left 83: 83: Converted 15 Constraints with virtual sites to connections, 7 left 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (2407 ms) 83: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (10911 ms total) 83: 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents converged to Fmax < 10 in 1 steps 83: Potential Energy = -9.74257075835450e-01 83: Maximum force = 4.01322929015108e+00 on atom 3 83: Norm of force = 1.63839399694368e+00 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (687 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 4.01323e+00 on atom 3 83: F-Norm = 1.63839e+00 83: 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 83: Potential Energy = -9.90642313893957e-01 83: Maximum force = 2.57812909491105e+00 on atom 3 83: Norm of force = 1.05251679559258e+00 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (859 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Number of degrees of freedom in T-Coupling group System is 33.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Generated 1 of the 1 non-bonded parameter combinations 83: 83: Excluding 1 bonded neighbours molecule type 'Argon' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (8 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Steepest Descents: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Steepest Descents did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 3.19395484891518e+02 83: Maximum force = 9.97041707197911e+03 on atom 9 83: Norm of force = 4.62274878665467e+03 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1295 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 83: Using 2 MPI threads 83: 83: Non-default thread affinity set, disabling internal thread affinity 83: 83: Using 2 OpenMP threads per tMPI thread 83: 83: 83: Polak-Ribiere Conjugate Gradients: 83: Tolerance (Fmax) = 1.00000e+01 83: Number of steps = 4 83: F-max = 2.41672e+04 on atom 10 83: F-Norm = 1.19357e+04 83: 83: 83: Energy minimization reached the maximum number of steps before the forces 83: reached the requested precision Fmax < 10. 83: 83: writing lowest energy coordinates. 83: 83: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 83: Potential Energy = 1.56258793899479e+02 83: Maximum force = 7.50181017480397e+03 on atom 9 83: Norm of force = 3.61390332564874e+03 83: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1823 ms) 83: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 83: 83: Generating 1-4 interactions: fudge = 1 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 83: COM removal frequency is set to (4). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Generated 20503 of the 20503 non-bonded parameter combinations 83: 83: Generated 17396 of the 20503 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'Glycine' 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (189 ms) 83: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (4865 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 12 tests from 2 test suites ran. (15808 ms total) 83: [ PASSED ] 12 tests. 83/103 Test #83: Minimize2RankTests ........................ Passed 15.84 sec test 84 Start 84: MdrunNonIntegratorTests 84: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 84: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 84: Test timeout computed to be: 600 84: [==========] Running 53 tests from 5 test suites. 84: [----------] Global test environment set-up. 84: [----------] 1 test from NonbondedBenchTest 84: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 84: System size: 3000 atoms 84: Cut-off radius: 1 nm 84: Number of threads: 1 84: Number of iterations: 1 84: Compute energies: no 84: Ewald excl. corr.: analytical 84: 84: Coulomb LJ comb. SIMD intmod. Mcycles Mcycles/it. pairs/cycle 84: total useful 84: Ewald all geom. no PotShift 0.064 0.0643 18.5024 9.7886 84: [ OK ] NonbondedBenchTest.BasicEndToEndTest (141 ms) 84: [----------] 1 test from NonbondedBenchTest (141 ms total) 84: 84: [----------] 5 tests from NormalModesWorks/NormalModesTest 84: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 15.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Small system size (N=6), using full Hessian format. 84: Allocating Hessian memory... 84: 84: starting normal mode calculation '2 scaled waters' 84: 12 steps. 84: 84: Maximum force: 9.96989e-06 84: 84: 84: Writing Hessian... 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Reading double precision matrix generated by GROMACS 2026.2-Debian_2026.2_2 84: 84: Diagonalizing to find vectors 7 through 18... 84: Writing eigenvalues... 84: 84: Writing average structure & eigenvectors 7--18 to eigenvec.trr 84: Generated 3 of the 3 non-bonded parameter combinations 84: 84: Generated 3 of the 3 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: This run will generate roughly 0 Mb of data 84: There are: 6 Atoms 84: Using begin = 7 and end = 18 84: Full matrix storage format, nrow=18, ncols=18 84: Writing eigenfrequencies - negative eigenvalues will be set to zero. 84: Cannot compute entropy when -first = 7 84: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (57 ms) 84: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 1 84: 84: NOTE 2 [file villin.top, line 2452]: 84: System has non-zero total charge: -2.000000 84: Total charge should normally be an integer. See 84: https://manual.gromacs.org/current/user-guide/floating-point.html 84: for discussion on how close it should be to an integer. 84: 84: 84: 84: Number of degrees of freedom in T-Coupling group System is 765.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Small system size (N=256), using full Hessian format. 84: Allocating Hessian memory... 84: 84: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 84: 512 steps. 84: 84: Maximum force: 6.97568e-04 84: 84: 84: Writing Hessian... 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Reading double precision matrix generated by GROMACS 2026.2-Debian_2026.2_2 84: 84: Diagonalizing to find vectors 7 through 50... 84: Writing eigenvalues... 84: 84: Writing average structure & eigenvectors 7--50 to eigenvec.trr 84: Generated 20503 of the 20503 non-bonded parameter combinations 84: 84: Generated 17396 of the 20503 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 84: 84: This run will generate roughly 0 Mb of data 84: There are: 256 Atoms 84: Using begin = 7 and end = 50 84: Full matrix storage format, nrow=768, ncols=768 84: Writing eigenfrequencies - negative eigenvalues will be set to zero. 84: Cannot compute entropy when -first = 7 84: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (4699 ms) 84: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 15.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Small system size (N=6), using full Hessian format. 84: Allocating Hessian memory... 84: 84: starting normal mode calculation 'flex spc dimer' 84: 12 steps. 84: 84: Maximum force: 3.36401e-04 84: 84: 84: Writing Hessian... 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Reading double precision matrix generated by GROMACS 2026.2-Debian_2026.2_2 84: 84: Diagonalizing to find vectors 7 through 18... 84: Writing eigenvalues... 84: 84: Writing average structure & eigenvectors 7--18 to eigenvec.trr 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: This run will generate roughly 0 Mb of data 84: There are: 6 Atoms 84: Using begin = 7 and end = 18 84: Full matrix storage format, nrow=18, ncols=18 84: Writing eigenfrequencies - negative eigenvalues will be set to zero. 84: Cannot compute entropy when -first = 7 84: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (1071 ms) 84: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 6.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 84: COM removal frequency is set to (4). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Small system size (N=3), using full Hessian format. 84: Allocating Hessian memory... 84: 84: starting normal mode calculation '1 TIP5P' 84: 6 steps. 84: 84: Maximum force: 2.42882e-04 84: 84: 84: Writing Hessian... 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Reading double precision matrix generated by GROMACS 2026.2-Debian_2026.2_2 84: 84: Diagonalizing to find vectors 7 through 9... 84: Writing eigenvalues... 84: 84: Writing average structure & eigenvectors 7--9 to eigenvec.trr 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: This run will generate roughly 0 Mb of data 84: There are: 3 Atoms 84: There are: 2 VSites 84: Using begin = 7 and end = 9 84: Full matrix storage format, nrow=9, ncols=9 84: Writing eigenfrequencies - negative eigenvalues will be set to zero. 84: Cannot compute entropy when -first = 7 84: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (1108 ms) 84: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 84: Number of degrees of freedom in T-Coupling group System is 15.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Update groups can not be used for this system because the construction atoms of a virtual site are only partly with a group of constrained atoms 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: 84: Small system size (N=6), using full Hessian format. 84: Allocating Hessian memory... 84: 84: starting normal mode calculation 'sw dimer' 84: 12 steps. 84: 84: Maximum force: 1.07599e-03 84: The force is probably not small enough to ensure that you are at a minimum. 84: Be aware that negative eigenvalues may occur 84: when the resulting matrix is diagonalized. 84: 84: 84: Writing Hessian... 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Reading double precision matrix generated by GROMACS 2026.2-Debian_2026.2_2 84: 84: Diagonalizing to find vectors 7 through 18... 84: Writing eigenvalues... 84: 84: Writing average structure & eigenvectors 7--18 to eigenvec.trr 84: Generated 6 of the 10 non-bonded parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SW' 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: This run will generate roughly 0 Mb of data 84: There are: 6 Atoms 84: There are: 2 Shells 84: There are: 2 VSites 84: 84: NOTE: in the current version shell prediction during the crun is disabled 84: 84: Using begin = 7 and end = 18 84: Full matrix storage format, nrow=18, ncols=18 84: Writing eigenfrequencies - negative eigenvalues will be set to zero. 84: Cannot compute entropy when -first = 7 84: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (18 ms) 84: [----------] 5 tests from NormalModesWorks/NormalModesTest (6955 ms total) 84: 84: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.016 0.008 197.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 183.438 0.131 0.471 0.025 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 84: 84: trr version: GMX_trn_file (double precision) 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 12 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 194.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1282.655 0.019 0.067 0.178 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (28 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 68.810 K for 84: determining the Verlet buffer size 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: NOTE: 26 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.037 0.019 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 78.541 0.306 1.100 0.011 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 12 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 194.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1410.715 0.017 0.061 0.196 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (41 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.013 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 113.765 0.211 0.759 0.016 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 15 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 194.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1467.157 0.016 0.059 0.204 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (32 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Number of degrees of freedom in T-Coupling group System is 33.00 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Argon' 84: 16 steps, 0.0 ps. 84: Generated 1 of the 1 non-bonded parameter combinations 84: 84: Excluding 1 bonded neighbours molecule type 'Argon' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.026 0.013 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 112.829 0.213 0.766 0.016 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 52 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.009 199.4 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 166.005 0.145 0.520 0.023 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (41 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.087 0.044 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 33.670 0.713 2.566 0.006 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 13 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 194.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1397.594 0.017 0.062 0.243 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (1057 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.090 0.045 199.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 32.770 0.732 2.637 0.006 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 194.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1226.233 0.020 0.070 0.213 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (1086 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.087 0.043 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 33.885 0.708 2.550 0.006 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 12 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 195.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1146.584 0.021 0.075 0.199 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (1097 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.087 0.044 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 33.554 0.715 2.575 0.006 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 20 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 195.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 1040.993 0.023 0.083 0.181 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (1083 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 84: NVE simulation: will use the initial temperature of 456.887 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 84: There are 9 non-linear virtual site constructions. Their contribution to 84: the energy error is approximated. In most cases this does not affect the 84: error significantly. 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Alanine dipeptide in vacuo' 84: 16 steps, 0.0 ps. 84: Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.009 197.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 164.938 0.146 0.524 0.055 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 195.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 676.245 0.035 0.128 0.227 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (65 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 456.887 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 84: There are 9 non-linear virtual site constructions. Their contribution to 84: the energy error is approximated. In most cases this does not affect the 84: error significantly. 84: 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Alanine dipeptide in vacuo' 84: 16 steps, 0.0 ps. 84: Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.031 0.016 198.7 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 93.045 0.258 0.929 0.031 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 195.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 752.485 0.032 0.115 0.253 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (71 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 84: There are 9 non-linear virtual site constructions. Their contribution to 84: the energy error is approximated. In most cases this does not affect the 84: error significantly. 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 84: 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Alanine dipeptide in vacuo' 84: 16 steps, 0.0 ps. 84: Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.090 0.045 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 32.485 0.739 2.660 0.011 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 84: 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 195.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 767.388 0.031 0.113 0.258 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (382 ms) 84: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: 84: NOTE 2 [file unknown]: 84: You are using constraints on all bonds, whereas the forcefield has been 84: parametrized only with constraints involving hydrogen atoms. We suggest 84: using constraints = h-bonds instead, this will also improve performance. 84: 84: Number of degrees of freedom in T-Coupling group System is 23.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 84: There are 9 non-linear virtual site constructions. Their contribution to 84: the energy error is approximated. In most cases this does not affect the 84: error significantly. 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 84: 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'Alanine dipeptide in vacuo' 84: 16 steps, 0.0 ps. 84: Generated 2145 of the 2145 non-bonded parameter combinations 84: 84: Generated 2145 of the 2145 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 84: 84: turning all bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/alanine_vsite_vacuo.gro' 84: 84: Cleaning up constraints and constant bonded interactions with virtual sites 84: 84: Removed 18 Angles with virtual sites, 21 left 84: 84: Removed 10 Proper Dih.s with virtual sites, 44 left 84: 84: Converted 15 Constraints with virtual sites to connections, 7 left 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.020 0.010 198.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 146.353 0.164 0.590 0.049 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 84: 84: Update groups can not be used for this system because an incompatible virtual site type is used 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 11 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.004 0.002 195.4 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 703.425 0.034 0.123 0.236 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (144 ms) 84: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (5136 ms total) 84: 84: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.043 0.021 198.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 68.431 0.351 1.263 0.029 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 188.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 535.052 0.045 0.161 0.223 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (71 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.044 0.022 198.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 66.521 0.361 1.299 0.028 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 535.471 0.045 0.161 0.223 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (71 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.046 0.023 198.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 63.667 0.377 1.357 0.027 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.006 0.003 187.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 495.225 0.048 0.174 0.206 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (80 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.066 0.033 199.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 44.139 0.544 1.957 0.018 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 577.321 0.042 0.150 0.241 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (79 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.052 0.026 199.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 56.364 0.426 1.533 0.023 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 548.291 0.044 0.158 0.228 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (74 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.052 0.026 199.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 56.508 0.425 1.529 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 186.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 521.952 0.046 0.166 0.217 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (74 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.069 0.034 199.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 42.619 0.563 2.027 0.018 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.002 187.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 589.418 0.041 0.147 0.246 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (81 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.060 0.030 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 48.604 0.494 1.778 0.020 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 44 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.027 0.014 197.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 107.023 0.224 0.807 0.045 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (99 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.074 0.037 199.3 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 39.368 0.610 2.195 0.016 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 185.9 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 581.024 0.041 0.149 0.242 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (87 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.057 0.029 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 51.400 0.467 1.681 0.021 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 186.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 578.025 0.042 0.149 0.241 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (76 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.069 0.034 199.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 42.648 0.563 2.026 0.018 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 181.3 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 574.629 0.042 0.150 0.239 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (82 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.063 0.031 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 46.865 0.512 1.844 0.020 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 186.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 583.998 0.041 0.148 0.243 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (78 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.058 0.029 199.3 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 50.835 0.472 1.700 0.021 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 183.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 509.645 0.047 0.170 0.212 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (78 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.048 0.024 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 60.940 0.394 1.418 0.025 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 182.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 539.409 0.044 0.160 0.225 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (72 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.082 0.041 199.7 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 35.760 0.671 2.416 0.015 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 186.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 569.529 0.042 0.152 0.237 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (87 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.055 0.027 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 53.723 0.447 1.608 0.022 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.7 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 555.910 0.043 0.155 0.232 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (75 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.058 0.029 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 50.746 0.473 1.703 0.021 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 570.425 0.042 0.151 0.238 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (76 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.061 0.030 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 48.422 0.496 1.784 0.020 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 61 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.017 0.009 196.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 165.946 0.145 0.521 0.069 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (88 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.067 0.034 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 43.509 0.552 1.986 0.018 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 185.7 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 560.615 0.043 0.154 0.234 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (81 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.056 0.028 199.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 52.673 0.456 1.640 0.022 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 188.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 537.667 0.045 0.161 0.224 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (75 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.055 0.027 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 53.487 0.449 1.615 0.022 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 185.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 559.545 0.043 0.154 0.233 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (75 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 84: NVE simulation: will use the initial temperature of 294.908 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 294.908 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.051 0.026 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 56.908 0.422 1.518 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.4 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 548.877 0.044 0.157 0.229 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (74 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.054 0.027 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 53.664 0.447 1.610 0.022 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.006 0.003 187.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 494.549 0.049 0.175 0.206 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (108 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.057 0.028 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 51.580 0.465 1.675 0.021 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.002 186.8 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 596.610 0.040 0.145 0.249 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (107 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.054 0.027 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 53.914 0.445 1.603 0.022 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.3 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 528.897 0.045 0.163 0.220 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (108 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.052 0.026 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 56.551 0.424 1.528 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 545.620 0.044 0.158 0.227 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (106 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.062 0.031 199.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 47.497 0.505 1.819 0.020 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 186.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 570.848 0.042 0.151 0.238 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (112 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.061 0.031 199.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 47.862 0.501 1.805 0.020 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 186.4 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 565.971 0.042 0.153 0.236 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (110 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.050 0.025 199.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 58.712 0.409 1.472 0.024 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: NOTE: 10 % of the run time was spent in pair search, 84: you might want to increase nstlist (this has no effect on accuracy) 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 186.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 583.555 0.041 0.148 0.243 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (104 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.058 0.029 199.2 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 50.746 0.473 1.703 0.021 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.6 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 519.574 0.046 0.166 0.216 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (110 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.077 0.039 199.4 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 37.939 0.633 2.277 0.016 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 553.016 0.043 0.156 0.230 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (120 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.055 0.028 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 52.956 0.453 1.632 0.022 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.4 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 546.055 0.044 0.158 0.228 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (108 ms) 84: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generating 1-4 interactions: fudge = 0.5 84: Number of degrees of freedom in T-Coupling group System is 79.00 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun '30 atom system in water' 84: 16 steps, 0.0 ps. 84: Generated 2485 of the 2485 non-bonded parameter combinations 84: 84: Generated 2485 of the 2485 1-4 parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'nonanol' 84: 84: turning H bonds into constraints... 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: turning H bonds into constraints... 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.050 0.025 199.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 59.045 0.406 1.463 0.025 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 84: 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting md rerun '30 atom system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 84: 84: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.005 0.003 187.0 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 571.325 0.042 0.151 0.238 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 84: 84: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (104 ms) 84: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (2948 ms total) 84: 84: [----------] 2 tests from Angles1/SimpleMdrunTest 84: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 84: 84: NOTE 1 [file angles1.top, line 72]: 84: In moleculetype 'butane' 4 atoms are not bound by a potential or 84: constraint to any other atom in the same moleculetype. Although 84: technically this might not cause issues in a simulation, this often means 84: that the user forgot to add a bond/potential/constraint or put multiple 84: molecules in the same moleculetype definition by mistake. Run with -v to 84: get information for each atom. 84: 84: Number of degrees of freedom in T-Coupling group System is 9.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 238.919 K for 84: determining the Verlet buffer size 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'This_incredible_box_of_butane' 84: 50 steps, 0.1 ps. 84: Generated 3 of the 3 non-bonded parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'butane' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/angles1.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.038 0.019 199.1 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 233.550 0.103 0.370 0.011 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 84: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (36 ms) 84: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 84: 84: NOTE 1 [file angles1.top, line 72]: 84: In moleculetype 'butane' 4 atoms are not bound by a potential or 84: constraint to any other atom in the same moleculetype. Although 84: technically this might not cause issues in a simulation, this often means 84: that the user forgot to add a bond/potential/constraint or put multiple 84: molecules in the same moleculetype definition by mistake. Run with -v to 84: get information for each atom. 84: 84: Number of degrees of freedom in T-Coupling group System is 9.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 238.919 K for 84: determining the Verlet buffer size 84: 84: 84: There were 2 NOTEs 84: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'This_incredible_box_of_butane' 84: 50 steps, 0.1 ps. 84: Generated 3 of the 3 non-bonded parameter combinations 84: 84: Excluding 3 bonded neighbours molecule type 'butane' 84: 84: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/angles1.gro' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.045 0.023 199.5 84: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 84: Performance: 193.746 0.124 0.446 0.009 84: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 84: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (38 ms) 84: [----------] 2 tests from Angles1/SimpleMdrunTest (75 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 53 tests from 5 test suites ran. (15320 ms total) 84: [ PASSED ] 53 tests. 84/103 Test #84: MdrunNonIntegratorTests ................... Passed 15.36 sec test 85 Start 85: MdrunTpiTests 85: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 3 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 3 tests from Simple/TpiTest 85: [ RUN ] Simple/TpiTest.ReproducesOutput/0 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 1308.00 85: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 85: Using 1 MPI thread 85: Using 1 OpenMP thread 85: 85: 85: NOTE: Thread affinity was not set. 85: Reading frames from gro file '216 water molecules', 648 atoms. 85: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 85: Last frame 0 time 0.000 85: Generated 331705 of the 331705 non-bonded parameter combinations 85: 85: Generated 331705 of the 331705 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Excluding 3 bonded neighbours molecule type 'methane' 85: Analysing residue names: 85: There are: 216 Water residues 85: There are: 1 Other residues 85: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] Simple/TpiTest.ReproducesOutput/0 (1103 ms) 85: [ RUN ] Simple/TpiTest.ReproducesOutput/1 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 1308.00 85: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 85: Using 1 MPI thread 85: Using 1 OpenMP thread 85: 85: 85: NOTE: Thread affinity was not set. 85: Reading frames from gro file '216 water molecules', 648 atoms. 85: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 85: Last frame 0 time 0.000 85: Generated 331705 of the 331705 non-bonded parameter combinations 85: 85: Generated 331705 of the 331705 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Excluding 3 bonded neighbours molecule type 'methane' 85: Analysing residue names: 85: There are: 216 Water residues 85: There are: 1 Other residues 85: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] Simple/TpiTest.ReproducesOutput/1 (1080 ms) 85: [ RUN ] Simple/TpiTest.ReproducesOutput/2 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 1308.00 85: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 85: Using 1 MPI thread 85: Using 1 OpenMP thread 85: 85: 85: NOTE: Thread affinity was not set. 85: Reading frames from gro file '216 water molecules', 648 atoms. 85: Reading frame 0 time 0.000 mu 6.203e+01 6.203e+01 85: Last frame 0 time 0.000 85: Generated 331705 of the 331705 non-bonded parameter combinations 85: 85: Generated 331705 of the 331705 1-4 parameter combinations 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: Excluding 3 bonded neighbours molecule type 'methane' 85: Analysing residue names: 85: There are: 216 Water residues 85: There are: 1 Other residues 85: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] Simple/TpiTest.ReproducesOutput/2 (1097 ms) 85: [----------] 3 tests from Simple/TpiTest (3282 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 3 tests from 1 test suite ran. (3301 ms total) 85: [ PASSED ] 3 tests. 85/103 Test #85: MdrunTpiTests ............................. Passed 3.33 sec test 86 Start 86: MdrunMpiTests 86: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 16 tests from 2 test suites. 86: [----------] Global test environment set-up. 86: [----------] 4 tests from MimicTest 86: [ RUN ] MimicTest.OneQuantumMol 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 86: For a correct single-point energy evaluation with nsteps = 0, use 86: continuation = yes to avoid constraining the input coordinates. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 21.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 86: NVE simulation with an initial temperature of zero: will use a Verlet 86: buffer of 10%. Check your energy drift! 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 86: 86: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 86: Reading frame 0 time 0.000 Last frame 0 time 0.000 86: 86: NOTE: 16 % of the run time was spent in domain decomposition, 86: 8 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.003 0.001 380.9 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 130.402 0.184 0.663 0.018 86: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 804782015 86: 86: Generated 10 of the 10 non-bonded parameter combinations 86: 86: Generated 10 of the 10 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] MimicTest.OneQuantumMol (17 ms) 86: [ RUN ] MimicTest.AllQuantumMol 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 86: For a correct single-point energy evaluation with nsteps = 0, use 86: continuation = yes to avoid constraining the input coordinates. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 21.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 86: NVE simulation with an initial temperature of zero: will use a Verlet 86: buffer of 10%. Check your energy drift! 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 86: 86: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 86: Reading frame 0 time 0.000 Last frame 0 time 0.000 86: 86: NOTE: 81 % of the run time was spent in domain decomposition, 86: 2 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: NOTE: 6 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.995 0.261 381.6 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 0.331 72.432 260.755 0.000 86: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1541003253 86: 86: Generated 10 of the 10 non-bonded parameter combinations 86: 86: Generated 10 of the 10 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] MimicTest.AllQuantumMol (858 ms) 86: [ RUN ] MimicTest.TwoQuantumMol 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 86: For a correct single-point energy evaluation with nsteps = 0, use 86: continuation = yes to avoid constraining the input coordinates. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 21.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 86: NVE simulation with an initial temperature of zero: will use a Verlet 86: buffer of 10%. Check your energy drift! 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro' 86: 86: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 86: Reading frame 0 time 0.000 Last frame 0 time 0.000 86: 86: NOTE: 79 % of the run time was spent in domain decomposition, 86: 3 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: NOTE: 6 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 1.054 0.276 382.6 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 0.313 76.557 275.604 0.000 86: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -4392517 86: 86: Generated 10 of the 10 non-bonded parameter combinations 86: 86: Generated 10 of the 10 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/4water.gro', all velocities are zero 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] MimicTest.TwoQuantumMol (855 ms) 86: [ RUN ] MimicTest.BondCuts 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 86: For a correct single-point energy evaluation with nsteps = 0, use 86: continuation = yes to avoid constraining the input coordinates. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 66.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 86: NVE simulation: will use the initial temperature of 300.368 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 86: 86: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 86: Reading frame 0 time 0.000 Last frame 0 time 0.000 86: 86: NOTE: 74 % of the run time was spent in domain decomposition, 86: 3 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: NOTE: 6 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.977 0.256 381.3 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 0.337 71.169 256.208 0.000 86: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -681610303 86: 86: Generated 2211 of the 2211 non-bonded parameter combinations 86: 86: Generated 2211 of the 2211 1-4 parameter combinations 86: 86: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/ala.gro' 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: [ OK ] MimicTest.BondCuts (860 ms) 86: [----------] 4 tests from MimicTest (2593 ms total) 86: 86: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 9.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 86: NVE simulation with an initial temperature of zero: will use a Verlet 86: buffer of 10%. Check your energy drift! 86: 86: 86: There was 1 NOTE 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 9.00 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group rest is 9.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 86: NVE simulation with an initial temperature of zero: will use a Verlet 86: buffer of 10%. Check your energy drift! 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: There were 2 NOTEs 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 9.00 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 86: The optimal PME mesh load for parallel simulations is below 0.5 86: and for highly parallel simulations between 0.25 and 0.33, 86: for higher performance, increase the cut-off and the PME grid spacing. 86: 86: 86: 86: There was 1 NOTE 86: Setting the LD random seed to 1069536638 86: 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 86: 86: This run will generate roughly 0 Mb of data 86: Setting the LD random seed to -109117889 86: 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: Setting the LD random seed to -152390684 86: 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 86: 86: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 86: 86: Estimate for the relative computational load of the PME mesh part: 1.00 86: 86: This run will generate roughly 0 Mb of data 86: Setting the LD random seed to -1099171283 86: 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2_and_vacuum.gro', all velocities are zero 86: 86: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 86: 86: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: Calculating fourier grid dimensions for X Y Z 86: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 86: 86: Estimate for the relative computational load of the PME mesh part: 1.00 86: 86: This run will generate roughly 0 Mb of data 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: 86: Dynamic load balancing report: 86: DLB was turned on during the run due to measured imbalance. 86: Average load imbalance: 9.2%. 86: The balanceable part of the MD step is 35%, load imbalance is computed from this. 86: Part of the total run time spent waiting due to load imbalance: 3.2%. 86: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 86: 86: 86: NOTE: 19 % of the run time was spent in domain decomposition, 86: 3 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: NOTE: 17 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 2.913 0.744 391.6 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 2.439 9.841 35.426 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (1333 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot have separate PME ranks when PME is not used 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot have separate PME ranks when PME is not used 86: Cannot use two separate PME ranks when there are less than four ranks total 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 86: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 86: 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: NOTE: 20 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 2.498 0.644 387.9 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 2.818 8.518 30.664 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (1235 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot have separate PME ranks when PME is not used 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot have separate PME ranks when PME is not used 86: Cannot use two separate PME ranks when there are less than four ranks total 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: 86: Dynamic load balancing report: 86: DLB was turned on during the run due to measured imbalance. 86: Average load imbalance: 18.1%. 86: The balanceable part of the MD step is 13%, load imbalance is computed from this. 86: Part of the total run time spent waiting due to load imbalance: 2.3%. 86: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 86: 86: 86: NOTE: 5 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 7.393 1.868 395.8 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 0.971 24.708 88.949 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (2503 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 2.163 0.556 388.8 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 3.262 7.357 26.486 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (943 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot use two separate PME ranks when there are less than four ranks total 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: NOTE: 7 % of the run time was spent communicating energies, 86: you might want to increase some nst* mdp options 86: 86: Core t (s) Wall t (s) (%) 86: Time: 6.994 1.764 396.5 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 1.029 23.333 83.999 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (2456 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 86: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 86: Changing nstlist from 10 to 100, rlist from 1 to 1 86: 86: Using 2 MPI threads 86: 86: Non-default thread affinity set, disabling internal thread affinity 86: 86: Using 2 OpenMP threads per tMPI thread 86: 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 2.048 0.528 387.9 86: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 86: Performance: 3.437 6.983 25.139 0.000 86: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (979 ms) 86: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 86: ./src/programs/mdrun/tests/domain_decomposition.cpp:387: Skipped 86: Test configuration is invalid: 86: Cannot use two separate PME ranks when there are less than four ranks total 86: 86: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 86: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (9453 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 16 tests from 2 test suites ran. (12140 ms total) 86: [ PASSED ] 10 tests. 86: [ SKIPPED ] 6 tests, listed below: 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 86: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 86/103 Test #86: MdrunMpiTests ............................. Passed 12.17 sec test 87 Start 87: MdrunMultiSimTests 87: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 2 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 2 tests from InNvt/MultiSimTerminationTest 87: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 87: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 87: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 87: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 87: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 2 tests from 1 test suite ran. (16 ms total) 87: [ PASSED ] 2 tests. 87: 87: YOU HAVE 4 DISABLED TESTS 87: 87/103 Test #87: MdrunMultiSimTests ........................ Passed 0.04 sec test 88 Start 88: MdrunMultiSimReplexTests 88: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" 88: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 1 test from 1 test suite. 88: [----------] Global test environment set-up. 88: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 88: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 88: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 88: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 88: 88: [----------] Global test environment tear-down 88: [==========] 1 test from 1 test suite ran. (16 ms total) 88: [ PASSED ] 1 test. 88: 88: YOU HAVE 4 DISABLED TESTS 88: 88/103 Test #88: MdrunMultiSimReplexTests .................. Passed 0.04 sec test 89 Start 89: MdrunMultiSimReplexEquivalenceTests 89: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 0 tests from 0 test suites. 89: [==========] 0 tests from 0 test suites ran. (0 ms total) 89: [ PASSED ] 0 tests. 89: 89: YOU HAVE 10 DISABLED TESTS 89: 89/103 Test #89: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.03 sec test 90 Start 90: MdrunMpi1RankPmeTests 90: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 90: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 90: Test timeout computed to be: 600 90: [==========] Running 19 tests from 1 test suite. 90: [----------] Global test environment set-up. 90: [----------] 19 tests from ReproducesEnergies/PmeTest 90: Number of degrees of freedom in T-Coupling group rest is 12.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 90: NVE simulation: will use the initial temperature of 1046.791 K for 90: determining the Verlet buffer size 90: 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: There were 2 NOTEs 90: 90: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 90: For a correct single-point energy evaluation with nsteps = 0, use 90: continuation = yes to avoid constraining the input coordinates. 90: 90: Number of degrees of freedom in T-Coupling group rest is 13.00 90: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 90: 90: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 90: NVE simulation: will use the initial temperature of 966.268 K for 90: determining the Verlet buffer size 90: 90: 90: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 90: The optimal PME mesh load for parallel simulations is below 0.5 90: and for highly parallel simulations between 0.25 and 0.33, 90: for higher performance, increase the cut-off and the PME grid spacing. 90: 90: 90: 90: There were 3 NOTEs 90: Setting the LD random seed to -1083251208 90: 90: Generated 8 of the 10 non-bonded parameter combinations 90: 90: Excluding 2 bonded neighbours molecule type 'Methanol' 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 90: 90: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 90: 90: Estimate for the relative computational load of the PME mesh part: 1.00 90: 90: This run will generate roughly 0 Mb of data 90: Setting the LD random seed to 1062579966 90: 90: Generated 8 of the 10 non-bonded parameter combinations 90: 90: Excluding 2 bonded neighbours molecule type 'Methanol' 90: 90: Excluding 2 bonded neighbours molecule type 'SOL' 90: 90: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 90: 90: Searching the wall atom type(s) 90: 90: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 90: 90: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 90: 90: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 90: 90: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 90: 90: Note that mdrun will redetermine rlist based on the actual pair-list setup 90: Calculating fourier grid dimensions for X Y Z 90: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 90: 90: Estimate for the relative computational load of the PME mesh part: 1.00 90: 90: This run will generate roughly 0 Mb of data 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 90: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'spc-and-methanol' 90: 20 steps, 0.0 ps. 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.076 0.038 199.4 90: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 90: Performance: 47.696 0.503 1.811 0.003 90: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (59 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 90: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'spc-and-methanol' 90: 20 steps, 0.0 ps. 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.057 0.029 199.3 90: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 90: Performance: 62.882 0.382 1.374 0.004 90: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (40 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: it targets GPU execution of FFT work, which is not supported in the current build 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 90: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'spc-and-methanol' 90: 0 steps, 0.0 ps. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.011 0.006 195.1 90: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 90: Performance: 15.467 1.552 5.586 0.001 90: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 90: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (42 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: it targets GPU execution of FFT work, which is not supported in the current build 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: it targets GPU execution, but no compatible devices were detected 90: it targets GPU execution of FFT work, which is not supported in the current build 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets using PME rank(s) but the simulation is using only one rank 90: it targets GPU execution, but no compatible devices were detected 90: it targets GPU execution of FFT work, which is not supported in the current build 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 90: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 90: Can not increase nstlist because an NVE ensemble is used 90: Using 1 MPI thread 90: Using 2 OpenMP threads 90: 90: 90: NOTE: The number of threads is not equal to the number of (logical) cpus 90: and the -pin option is set to auto: will not pin threads to cpus. 90: This can lead to significant performance degradation. 90: Consider using -pin on (and -pinoffset in case you run multiple jobs). 90: starting mdrun 'spc-and-methanol' 90: 20 steps, 0.0 ps. 90: 90: Writing final coordinates. 90: 90: Core t (s) Wall t (s) (%) 90: Time: 0.069 0.035 199.4 90: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 90: Performance: 52.287 0.459 1.652 0.004 90: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 90: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (47 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 90: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 90: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 90: Test is being skipped because: 90: it targets GPU execution, but no compatible devices were detected 90: it targets GPU execution of FFT work, which is not supported in the current build 90: PME GPU does not support: 90: Double-precision build of GROMACS. 90: Non-GPU build of GROMACS. 90: Current GPU backend. 90: 90: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 90: [----------] 19 tests from ReproducesEnergies/PmeTest (194 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 19 tests from 1 test suite ran. (230 ms total) 90: [ PASSED ] 4 tests. 90: [ SKIPPED ] 15 tests, listed below: 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 90: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 90/103 Test #90: MdrunMpi1RankPmeTests ..................... Passed 0.26 sec test 91 Start 91: MdrunMpi2RankPmeTests 91: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 91: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 91: Test timeout computed to be: 600 91: [==========] Running 19 tests from 1 test suite. 91: [----------] Global test environment set-up. 91: [----------] 19 tests from ReproducesEnergies/PmeTest 91: Number of degrees of freedom in T-Coupling group rest is 12.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 1046.791 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 2 NOTEs 91: 91: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: For a correct single-point energy evaluation with nsteps = 0, use 91: continuation = yes to avoid constraining the input coordinates. 91: 91: Number of degrees of freedom in T-Coupling group rest is 13.00 91: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 91: 91: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: NVE simulation: will use the initial temperature of 966.268 K for 91: determining the Verlet buffer size 91: 91: 91: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 91: The optimal PME mesh load for parallel simulations is below 0.5 91: and for highly parallel simulations between 0.25 and 0.33, 91: for higher performance, increase the cut-off and the PME grid spacing. 91: 91: 91: 91: There were 3 NOTEs 91: Setting the LD random seed to -592068681 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: Setting the LD random seed to 402025979 91: 91: Generated 8 of the 10 non-bonded parameter combinations 91: 91: Excluding 2 bonded neighbours molecule type 'Methanol' 91: 91: Excluding 2 bonded neighbours molecule type 'SOL' 91: 91: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 91: 91: Searching the wall atom type(s) 91: 91: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 91: 91: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 91: 91: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 91: 91: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 91: 91: Note that mdrun will redetermine rlist based on the actual pair-list setup 91: Calculating fourier grid dimensions for X Y Z 91: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 91: 91: Estimate for the relative computational load of the PME mesh part: 1.00 91: 91: This run will generate roughly 0 Mb of data 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: 91: Dynamic load balancing report: 91: DLB was off during the run due to low measured imbalance. 91: Average load imbalance: 6.6%. 91: The balanceable part of the MD step is 9%, load imbalance is computed from this. 91: Part of the total run time spent waiting due to load imbalance: 0.6%. 91: 91: 91: NOTE: 28 % of the run time was spent communicating energies, 91: you might want to increase some nst* mdp options 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.145 0.036 398.6 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 49.718 0.483 1.738 0.003 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (64 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: 91: Dynamic load balancing report: 91: DLB was turned on during the run due to measured imbalance. 91: Average load imbalance: 32.6%. 91: The balanceable part of the MD step is 19%, load imbalance is computed from this. 91: Part of the total run time spent waiting due to load imbalance: 6.2%. 91: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 91: 91: NOTE: 6.2 % of the available CPU time was lost due to load imbalance 91: in the domain decomposition. 91: You can consider manually changing the decomposition (option -dd); 91: e.g. by using fewer domains along the box dimension in which there is 91: considerable inhomogeneity in the simulated system. 91: 91: NOTE: 12 % of the run time was spent communicating energies, 91: you might want to increase some nst* mdp options 91: 91: Core t (s) Wall t (s) (%) 91: Time: 9.792 2.464 397.4 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 0.736 32.592 117.332 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (3104 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 0 steps, 0.0 ps. 91: 91: NOTE: 25 % of the run time was spent in domain decomposition, 91: 2 % of the run time was spent in pair search, 91: you might want to increase nstlist (this has no effect on accuracy) 91: 91: NOTE: 6 % of the run time was spent communicating energies, 91: you might want to increase some nst* mdp options 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.817 0.220 371.7 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 0.393 61.085 219.905 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (899 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 2.258 0.580 389.3 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 3.129 7.671 27.614 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (979 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 2.216 0.570 388.9 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 3.185 7.535 27.127 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (987 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 0 steps, 0.0 ps. 91: 91: Core t (s) Wall t (s) (%) 91: Time: 0.161 0.056 287.4 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 1.546 15.520 55.873 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (521 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 91: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 91: Can not increase nstlist because an NVE ensemble is used 91: Using 2 MPI threads 91: 91: Non-default thread affinity set, disabling internal thread affinity 91: 91: Using 2 OpenMP threads per tMPI thread 91: 91: starting mdrun 'spc-and-methanol' 91: 20 steps, 0.0 ps. 91: 91: Writing final coordinates. 91: 91: 91: Dynamic load balancing report: 91: DLB was turned on during the run due to measured imbalance. 91: Average load imbalance: 34.2%. 91: The balanceable part of the MD step is 19%, load imbalance is computed from this. 91: Part of the total run time spent waiting due to load imbalance: 6.5%. 91: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 91: 91: NOTE: 6.5 % of the available CPU time was lost due to load imbalance 91: in the domain decomposition. 91: You can consider manually changing the decomposition (option -dd); 91: e.g. by using fewer domains along the box dimension in which there is 91: considerable inhomogeneity in the simulated system. 91: 91: NOTE: 13 % of the run time was spent communicating energies, 91: you might want to increase some nst* mdp options 91: 91: Core t (s) Wall t (s) (%) 91: Time: 9.600 2.416 397.4 91: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 91: Performance: 0.751 31.957 115.045 0.000 91: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 91: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (3076 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 91: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 91: Test is being skipped because: 91: it targets GPU execution, but no compatible devices were detected 91: it targets PME decomposition, but that is not supported 91: it targets GPU execution of FFT work, which is not supported in the current build 91: PME GPU does not support: 91: Double-precision build of GROMACS. 91: Non-GPU build of GROMACS. 91: Current GPU backend. 91: 91: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 91: [----------] 19 tests from ReproducesEnergies/PmeTest (9638 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 19 tests from 1 test suite ran. (9674 ms total) 91: [ PASSED ] 7 tests. 91: [ SKIPPED ] 12 tests, listed below: 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 91: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 91/103 Test #91: MdrunMpi2RankPmeTests ..................... Passed 9.70 sec test 92 Start 92: MdrunMpi4RankPmeTests 92: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "1" "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunMpi4RankPmeTests.xml" 92: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 92: Test timeout computed to be: 600 92: [==========] Running 19 tests from 1 test suite. 92: [----------] Global test environment set-up. 92: [----------] 19 tests from ReproducesEnergies/PmeTest 92: Number of degrees of freedom in T-Coupling group rest is 12.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 1046.791 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 2 NOTEs 92: 92: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: For a correct single-point energy evaluation with nsteps = 0, use 92: continuation = yes to avoid constraining the input coordinates. 92: 92: Number of degrees of freedom in T-Coupling group rest is 13.00 92: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 92: 92: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: NVE simulation: will use the initial temperature of 966.268 K for 92: determining the Verlet buffer size 92: 92: 92: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 92: The optimal PME mesh load for parallel simulations is below 0.5 92: and for highly parallel simulations between 0.25 and 0.33, 92: for higher performance, increase the cut-off and the PME grid spacing. 92: 92: 92: 92: There were 3 NOTEs 92: Setting the LD random seed to -537969681 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: Setting the LD random seed to -2097545 92: 92: Generated 8 of the 10 non-bonded parameter combinations 92: 92: Excluding 2 bonded neighbours molecule type 'Methanol' 92: 92: Excluding 2 bonded neighbours molecule type 'SOL' 92: 92: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc-and-methanol.gro' 92: 92: Searching the wall atom type(s) 92: 92: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 92: 92: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 92: 92: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 92: 92: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 92: 92: Note that mdrun will redetermine rlist based on the actual pair-list setup 92: Calculating fourier grid dimensions for X Y Z 92: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 92: 92: Estimate for the relative computational load of the PME mesh part: 1.00 92: 92: This run will generate roughly 0 Mb of data 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was off during the run due to low measured imbalance. 92: Average load imbalance: 14.0%. 92: The balanceable part of the MD step is 7%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 0.9%. 92: 92: 92: NOTE: 61 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.323 0.081 399.3 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 22.405 1.071 3.856 0.002 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_cpu (220 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 16.2%. 92: The balanceable part of the MD step is 24%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 3.8%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: 92: 92: NOTE: 23 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 18.048 4.560 395.8 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.398 60.317 217.142 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_0__pme_auto.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_auto (6199 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: NOTE: 30 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 14 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 1.409 0.401 351.7 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.216 111.271 400.574 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_0__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_cpu (2069 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 10.5%. 92: The balanceable part of the MD step is 62%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 6.5%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: Average PME mesh/force load: 0.134 92: Part of the total run time spent waiting due to PP/PME imbalance: 4.9 % 92: 92: NOTE: 6.5 % of the available CPU time was lost due to load imbalance 92: in the domain decomposition. 92: You can consider manually changing the decomposition (option -dd); 92: e.g. by using fewer domains along the box dimension in which there is 92: considerable inhomogeneity in the simulated system. 92: 92: NOTE: 15 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 34 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 6.944 1.780 390.1 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 1.019 23.545 84.760 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_cpu (3328 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 11.5%. 92: The balanceable part of the MD step is 60%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 6.9%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: Average PME mesh/force load: 0.192 92: Part of the total run time spent waiting due to PP/PME imbalance: 4.2 % 92: 92: NOTE: 6.9 % of the available CPU time was lost due to load imbalance 92: in the domain decomposition. 92: You can consider manually changing the decomposition (option -dd); 92: e.g. by using fewer domains along the box dimension in which there is 92: considerable inhomogeneity in the simulated system. 92: 92: NOTE: 15 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 33 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 7.208 1.846 390.5 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.983 24.419 87.907 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__notunepme__npme_1__pme_auto.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_auto (3395 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 0 steps, 0.0 ps. 92: 92: NOTE: 43 % of the run time was spent in domain decomposition, 92: 0 % of the run time was spent in pair search, 92: you might want to increase nstlist (this has no effect on accuracy) 92: 92: NOTE: 15 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 0.716 0.227 315.5 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.381 63.053 226.990 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls__notunepme__npme_1__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_cpu (1790 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu 92: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 92: Can not increase nstlist because an NVE ensemble is used 92: Using 4 MPI threads 92: 92: Non-default thread affinity set, disabling internal thread affinity 92: 92: Using 1 OpenMP thread per tMPI thread 92: 92: starting mdrun 'spc-and-methanol' 92: 20 steps, 0.0 ps. 92: 92: Writing final coordinates. 92: 92: 92: Dynamic load balancing report: 92: DLB was turned on during the run due to measured imbalance. 92: Average load imbalance: 12.2%. 92: The balanceable part of the MD step is 24%, load imbalance is computed from this. 92: Part of the total run time spent waiting due to load imbalance: 2.9%. 92: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 92: 92: 92: NOTE: 23 % of the run time was spent communicating energies, 92: you might want to increase some nst* mdp options 92: 92: Core t (s) Wall t (s) (%) 92: Time: 17.680 4.468 395.7 92: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 92: Performance: 0.406 59.100 212.762 0.000 92: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic__tunepme__npme_0__pme_cpu.edr as double precision energy file 92: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_cpu (6059 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu (0 ms) 92: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92: ./src/programs/mdrun/tests/pmetest.cpp:334: Skipped 92: Test is being skipped because: 92: it targets GPU execution, but no compatible devices were detected 92: it targets PME decomposition, but that is not supported 92: it targets GPU execution of FFT work, which is not supported in the current build 92: PME GPU does not support: 92: Double-precision build of GROMACS. 92: Non-GPU build of GROMACS. 92: Current GPU backend. 92: 92: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu (0 ms) 92: [----------] 19 tests from ReproducesEnergies/PmeTest (23069 ms total) 92: 92: [----------] Global test environment tear-down 92: [==========] 19 tests from 1 test suite ran. (23105 ms total) 92: [ PASSED ] 7 tests. 92: [ SKIPPED ] 12 tests, listed below: 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_0__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_0__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__notunepme__npme_1__pme_gpu__pmefft_auto 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls__notunepme__npme_1__pme_gpu__pmefft_gpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_cpu 92: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic__tunepme__npme_0__pme_gpu__pmefft_gpu 92/103 Test #92: MdrunMpi4RankPmeTests ..................... Passed 23.13 sec test 93 Start 93: MdrunCoordinationBasicTests1Rank 93: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 93: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 93: Test timeout computed to be: 1920 93: [==========] Running 1 test from 1 test suite. 93: [----------] Global test environment set-up. 93: [----------] 1 test from BasicPropagators/PeriodicActionsTest 93: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: Setting nstcalcenergy (100) equal to nstenergy (1) 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: There were 2 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.015 0.015 99.5 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 96.956 0.248 0.891 0.013 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: Setting nstcalcenergy (100) equal to nstenergy (1) 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: There were 2 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.006 0.006 98.8 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 258.544 0.093 0.334 0.036 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: Setting nstcalcenergy (100) equal to nstenergy (4) 93: 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 93: setting nstcomm equal to nstcalcenergy for less overhead 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: COM removal frequency is set to (1). 93: Other settings require a global communication frequency of 4. 93: Note that this will require additional global communication steps, 93: which will reduce performance when using multiple ranks. 93: Consider setting nstcomm to a multiple of 4. 93: 93: 93: There were 4 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.006 0.006 98.9 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 243.945 0.098 0.354 0.034 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 93: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 93: setting nstcomm equal to nstcalcenergy for less overhead 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: COM removal frequency is set to (1). 93: Other settings require a global communication frequency of 100. 93: Note that this will require additional global communication steps, 93: which will reduce performance when using multiple ranks. 93: Consider setting nstcomm to a multiple of 100. 93: 93: 93: There were 3 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.010 0.010 99.3 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 146.193 0.164 0.591 0.020 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 93: setting nstcomm equal to nstcalcenergy for less overhead 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: COM removal frequency is set to (1). 93: Other settings require a global communication frequency of 100. 93: Note that this will require additional global communication steps, 93: which will reduce performance when using multiple ranks. 93: Consider setting nstcomm to a multiple of 100. 93: 93: 93: There were 3 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.007 0.007 99.0 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 220.573 0.109 0.392 0.031 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 93: 93: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 93: setting nstcomm equal to nstcalcenergy for less overhead 93: 93: Number of degrees of freedom in T-Coupling group System is 33.00 93: 93: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: NVE simulation: will use the initial temperature of 68.810 K for 93: determining the Verlet buffer size 93: 93: 93: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 93: COM removal frequency is set to (1). 93: Other settings require a global communication frequency of 100. 93: Note that this will require additional global communication steps, 93: which will reduce performance when using multiple ranks. 93: Consider setting nstcomm to a multiple of 100. 93: 93: 93: There were 3 NOTEs 93: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 93: Can not increase nstlist because an NVE ensemble is used 93: Using 1 MPI thread 93: Using 1 OpenMP thread 93: 93: 93: NOTE: Thread affinity was not set. 93: starting mdrun 'Argon' 93: 16 steps, 0.0 ps. 93: Generated 1 of the 1 non-bonded parameter combinations 93: 93: Excluding 1 bonded neighbours molecule type 'Argon' 93: 93: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 93: 93: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 93: 93: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 93: 93: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 93: 93: Note that mdrun will redetermine rlist based on the actual pair-list setup 93: 93: This run will generate roughly 0 Mb of data 93: 93: Writing final coordinates. 93: 93: Core t (s) Wall t (s) (%) 93: Time: 0.012 0.012 99.4 93: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 93: Performance: 123.469 0.194 0.700 0.017 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 93: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 93: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (133 ms) 93: [----------] 1 test from BasicPropagators/PeriodicActionsTest (133 ms total) 93: 93: [----------] Global test environment tear-down 93: [==========] 1 test from 1 test suite ran. (149 ms total) 93: [ PASSED ] 1 test. 93/103 Test #93: MdrunCoordinationBasicTests1Rank .......... Passed 0.18 sec test 94 Start 94: MdrunCoordinationBasicTests2Ranks 94: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 94: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 94: Test timeout computed to be: 1920 94: [==========] Running 1 test from 1 test suite. 94: [----------] Global test environment set-up. 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest 94: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.9%. 94: The balanceable part of the MD step is 57%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 1.1%. 94: 94: 94: NOTE: 45 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.030 0.015 198.6 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 97.448 0.246 0.887 0.014 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (1) 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: There were 2 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 2.4%. 94: The balanceable part of the MD step is 56%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 1.4%. 94: 94: 94: NOTE: 44 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.022 0.011 198.3 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 133.598 0.180 0.647 0.019 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: Setting nstcalcenergy (100) equal to nstenergy (4) 94: 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 4. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 4. 94: 94: 94: There were 4 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.6%. 94: The balanceable part of the MD step is 51%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.8%. 94: 94: 94: NOTE: 44 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.016 0.008 197.7 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 186.053 0.129 0.464 0.026 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.7%. 94: The balanceable part of the MD step is 49%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.8%. 94: 94: 94: NOTE: 47 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.030 0.015 198.6 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 96.012 0.250 0.900 0.013 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.4%. 94: The balanceable part of the MD step is 49%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.7%. 94: 94: 94: NOTE: 47 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.032 0.016 198.8 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 92.207 0.260 0.937 0.013 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: 94: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 94: setting nstcomm equal to nstcalcenergy for less overhead 94: 94: Number of degrees of freedom in T-Coupling group System is 33.00 94: 94: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: NVE simulation: will use the initial temperature of 68.810 K for 94: determining the Verlet buffer size 94: 94: 94: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 94: COM removal frequency is set to (1). 94: Other settings require a global communication frequency of 100. 94: Note that this will require additional global communication steps, 94: which will reduce performance when using multiple ranks. 94: Consider setting nstcomm to a multiple of 100. 94: 94: 94: There were 3 NOTEs 94: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 94: Can not increase nstlist because an NVE ensemble is used 94: Using 2 MPI threads 94: Using 1 OpenMP thread per tMPI thread 94: 94: 94: NOTE: The number of threads is not equal to the number of (logical) cpus 94: and the -pin option is set to auto: will not pin threads to cpus. 94: This can lead to significant performance degradation. 94: Consider using -pin on (and -pinoffset in case you run multiple jobs). 94: starting mdrun 'Argon' 94: 16 steps, 0.0 ps. 94: Generated 1 of the 1 non-bonded parameter combinations 94: 94: Excluding 1 bonded neighbours molecule type 'Argon' 94: 94: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 94: 94: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 94: 94: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 94: 94: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 94: 94: Note that mdrun will redetermine rlist based on the actual pair-list setup 94: 94: This run will generate roughly 0 Mb of data 94: 94: Writing final coordinates. 94: 94: 94: Dynamic load balancing report: 94: DLB was off during the run due to low measured imbalance. 94: Average load imbalance: 1.5%. 94: The balanceable part of the MD step is 51%, load imbalance is computed from this. 94: Part of the total run time spent waiting due to load imbalance: 0.7%. 94: 94: 94: NOTE: 47 % of the run time was spent communicating energies, 94: you might want to increase some nst* mdp options 94: 94: Core t (s) Wall t (s) (%) 94: Time: 0.028 0.014 198.6 94: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 94: Performance: 103.244 0.232 0.837 0.014 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 94: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 94: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (164 ms) 94: [----------] 1 test from BasicPropagators/PeriodicActionsTest (164 ms total) 94: 94: [----------] Global test environment tear-down 94: [==========] 1 test from 1 test suite ran. (180 ms total) 94: [ PASSED ] 1 test. 94/103 Test #94: MdrunCoordinationBasicTests2Ranks ......... Passed 0.21 sec test 95 Start 95: MdrunCoordinationCouplingTests1Rank 95: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 95: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 95: Test timeout computed to be: 1920 95: [==========] Running 25 tests from 1 test suite. 95: [----------] Global test environment set-up. 95: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.026 0.026 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 55.672 0.431 1.552 0.008 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 152.207 0.158 0.568 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 4. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 4. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 145.513 0.165 0.594 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 100.588 0.239 0.859 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 126.457 0.190 0.683 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 146.412 0.164 0.590 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (159 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.020 0.020 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 73.988 0.324 1.168 0.010 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.008 0.008 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 185.739 0.129 0.465 0.026 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 158.431 0.151 0.545 0.022 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 137.876 0.174 0.627 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 134.136 0.179 0.644 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 126.131 0.190 0.685 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (145 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 102.562 0.234 0.842 0.014 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 111.180 0.216 0.777 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 145.654 0.165 0.593 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.017 0.017 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 88.376 0.272 0.978 0.012 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 92.809 0.259 0.931 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.034 0.034 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 42.806 0.561 2.018 0.006 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (179 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.023 0.023 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 65.043 0.369 1.328 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 134.517 0.178 0.642 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 114.722 0.209 0.753 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 106.358 0.226 0.812 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 133.955 0.179 0.645 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 116.729 0.206 0.740 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (159 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.020 0.020 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 72.039 0.333 1.199 0.010 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 165.163 0.145 0.523 0.023 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 141.655 0.169 0.610 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 151.158 0.159 0.572 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 130.397 0.184 0.663 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 148.936 0.161 0.580 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (152 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 92.208 0.260 0.937 0.013 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.008 0.008 99.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 173.680 0.138 0.497 0.024 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 141.285 0.170 0.612 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 100.149 0.240 0.863 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 148.244 0.162 0.583 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 155.183 0.155 0.557 0.022 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (147 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.022 0.022 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 67.451 0.356 1.281 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 144.581 0.166 0.598 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 142.768 0.168 0.605 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 114.518 0.210 0.754 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 126.218 0.190 0.685 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 107.094 0.224 0.807 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (159 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.016 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 94.480 0.254 0.914 0.013 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 120.099 0.200 0.719 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 160.981 0.149 0.537 0.022 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 140.499 0.171 0.615 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 141.571 0.170 0.610 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 128.853 0.186 0.671 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (148 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 105.020 0.229 0.823 0.015 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.026 0.026 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 56.392 0.426 1.532 0.008 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 107.763 0.223 0.802 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 93.889 0.256 0.920 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.018 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 83.511 0.287 1.035 0.012 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.018 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 82.638 0.290 1.046 0.011 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (181 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 96.307 0.249 0.897 0.013 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.008 0.009 99.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 171.232 0.140 0.505 0.024 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 106.821 0.225 0.809 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.008 0.008 98.9 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 177.539 0.135 0.487 0.025 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 93.615 0.256 0.923 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 104.015 0.231 0.831 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (153 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 103.978 0.231 0.831 0.014 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 115.072 0.209 0.751 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.007 0.007 99.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 201.980 0.119 0.428 0.028 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 109.889 0.218 0.786 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.010 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 154.498 0.155 0.559 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.026 0.026 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 57.420 0.418 1.505 0.008 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (162 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.020 0.020 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 73.717 0.326 1.172 0.010 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 147.573 0.163 0.585 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.005 0.005 98.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 273.816 0.088 0.316 0.038 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 109.384 0.219 0.790 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 109.693 0.219 0.788 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 95: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 95: 1 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 124.043 0.193 0.697 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (152 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 93.132 0.258 0.928 0.013 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 128.875 0.186 0.670 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 4. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 4. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 167.044 0.144 0.517 0.023 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 96.778 0.248 0.893 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 102.937 0.233 0.839 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 89.061 0.269 0.970 0.012 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (159 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 110.502 0.217 0.782 0.015 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 134.628 0.178 0.642 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 98.8 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 148.649 0.161 0.581 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 120.275 0.200 0.718 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 133.807 0.179 0.646 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.012 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 127.567 0.188 0.677 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (146 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 99.885 0.240 0.865 0.014 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 111.254 0.216 0.777 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 146.531 0.164 0.590 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 124.782 0.192 0.692 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 147.690 0.163 0.585 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 150.138 0.160 0.575 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (149 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.021 0.021 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 69.192 0.347 1.249 0.010 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 100.762 0.238 0.857 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 124.918 0.192 0.692 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 103.212 0.233 0.837 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 119.327 0.201 0.724 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 132.958 0.181 0.650 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (163 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.022 0.022 99.8 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 65.480 0.367 1.319 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 121.448 0.198 0.711 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 4. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 4. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 126.436 0.190 0.683 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 91.230 0.263 0.947 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 116.183 0.207 0.744 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 100. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 100. 95: 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 105.859 0.227 0.816 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (164 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.020 0.020 99.8 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 72.177 0.333 1.197 0.010 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.013 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 116.981 0.205 0.739 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 121.530 0.197 0.711 0.017 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.017 0.018 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 83.659 0.287 1.033 0.012 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 103.663 0.232 0.833 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 147.249 0.163 0.587 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (163 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 97.829 0.245 0.883 0.014 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 129.056 0.186 0.669 0.018 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.009 0.009 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 156.942 0.153 0.551 0.022 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 115.599 0.208 0.747 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 110.635 0.217 0.781 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 95: NVE simulation: will use the initial temperature of 68.810 K for 95: determining the Verlet buffer size 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Can not increase nstlist because an NVE ensemble is used 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 147.825 0.162 0.584 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (147 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.018 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 80.368 0.299 1.075 0.011 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.008 0.008 98.8 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 193.134 0.124 0.447 0.027 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.011 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 139.094 0.173 0.621 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 117.996 0.203 0.732 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 148.692 0.161 0.581 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 117.825 0.204 0.733 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (148 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.018 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 81.315 0.295 1.063 0.011 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.006 0.006 98.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 227.119 0.106 0.380 0.032 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 136.251 0.176 0.634 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.015 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 100.775 0.238 0.857 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.014 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 108.326 0.222 0.798 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 95: The Berendsen barostat does not generate any strictly correct ensemble, 95: and should not be used for new production simulations (in our opinion). 95: We recommend using the C-rescale barostat instead. 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: 95: There was 1 WARNING 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 95.383 0.252 0.906 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (157 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.023 0.023 99.6 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 64.514 0.372 1.339 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.2 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 152.237 0.158 0.568 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 114.490 0.210 0.755 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.019 0.019 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 77.168 0.311 1.120 0.011 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.018 0.018 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 82.033 0.293 1.053 0.011 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.012 0.012 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 118.699 0.202 0.728 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (172 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.022 0.023 99.7 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 65.245 0.368 1.324 0.009 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 145.140 0.165 0.595 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.011 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 138.962 0.173 0.622 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 90.432 0.265 0.955 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 147.207 0.163 0.587 0.020 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 2 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.1 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 134.358 0.179 0.643 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (158 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 90.460 0.265 0.955 0.013 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There were 3 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 102.519 0.234 0.843 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 4 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.016 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 94.305 0.254 0.916 0.013 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 4 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.019 0.019 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 76.744 0.313 1.126 0.011 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 4 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.011 0.011 99.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 138.083 0.174 0.626 0.019 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: 95: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: MTTK coupling is deprecated and will soon be removed 95: 95: 95: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: for current Trotter decomposition methods with vv, nsttcouple and 95: nstpcouple must be equal. Both have been reset to 95: min(nsttcouple,nstpcouple) = 2 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 95: COM removal frequency is set to (5). 95: Other settings require a global communication frequency of 2. 95: Note that this will require additional global communication steps, 95: which will reduce performance when using multiple ranks. 95: Consider setting nstcomm to a multiple of 2. 95: 95: 95: There were 4 NOTEs 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.017 0.017 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 88.163 0.272 0.980 0.012 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (171 ms) 95: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 97.322 0.247 0.888 0.014 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (1) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.010 0.010 99.0 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 149.758 0.160 0.577 0.021 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: Setting nstcalcenergy (100) equal to nstenergy (4) 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.014 0.014 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 105.298 0.228 0.821 0.015 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 95: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.013 0.013 99.3 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 113.167 0.212 0.763 0.016 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.015 0.015 99.4 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 98.571 0.243 0.877 0.014 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 95: 95: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 95: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 95: setting nstcomm equal to nstcalcenergy for less overhead 95: 95: Number of degrees of freedom in T-Coupling group System is 33.00 95: 95: There was 1 NOTE 95: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 95: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 95: 95: Using 1 MPI thread 95: Using 1 OpenMP thread 95: 95: 95: NOTE: Thread affinity was not set. 95: starting mdrun 'Argon' 95: 16 steps, 0.0 ps. 95: Generated 1 of the 1 non-bonded parameter combinations 95: 95: Excluding 1 bonded neighbours molecule type 'Argon' 95: 95: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 95: 95: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 95: 95: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 95: 95: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 95: 95: Note that mdrun will redetermine rlist based on the actual pair-list setup 95: 95: This run will generate roughly 0 Mb of data 95: 95: Writing final coordinates. 95: 95: Core t (s) Wall t (s) (%) 95: Time: 0.016 0.016 99.5 95: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 95: Performance: 89.148 0.269 0.969 0.012 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 95: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 95: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (161 ms) 95: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (3966 ms total) 95: 95: [----------] Global test environment tear-down 95: [==========] 25 tests from 1 test suite ran. (3982 ms total) 95: [ PASSED ] 25 tests. 95/103 Test #95: MdrunCoordinationCouplingTests1Rank ....... Passed 4.01 sec test 96 Start 96: MdrunCoordinationCouplingTests2Ranks 96: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 96: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 96: Test timeout computed to be: 1920 96: [==========] Running 25 tests from 1 test suite. 96: [----------] Global test environment set-up. 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.1%. 96: The balanceable part of the MD step is 56%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.2%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.064 0.032 199.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 45.726 0.525 1.890 0.006 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.3%. 96: The balanceable part of the MD step is 52%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.2%. 96: 96: 96: NOTE: 50 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 1.042 0.521 200.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 2.818 8.517 30.660 0.000 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 3.6%. 96: The balanceable part of the MD step is 47%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.7%. 96: 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.084 0.042 199.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 34.897 0.688 2.476 0.005 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.8%. 96: The balanceable part of the MD step is 45%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.098 0.049 199.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 29.863 0.804 2.893 0.004 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.3%. 96: The balanceable part of the MD step is 44%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.0%. 96: 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.084 0.042 199.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 35.072 0.684 2.464 0.005 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.2%. 96: The balanceable part of the MD step is 45%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.0%. 96: 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.084 0.042 199.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 34.993 0.686 2.469 0.005 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1210 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.6%. 96: The balanceable part of the MD step is 58%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.9%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.094 0.047 199.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 31.219 0.769 2.768 0.004 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.2%. 96: The balanceable part of the MD step is 55%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.2%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.068 0.034 199.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 43.196 0.556 2.000 0.006 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.5%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.055 0.027 199.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 53.642 0.447 1.611 0.007 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.4%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.065 0.033 199.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 44.744 0.536 1.931 0.006 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.8%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.9%. 96: 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.121 0.061 199.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 24.168 0.993 3.575 0.003 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.3%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: NOTE: 49 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.153 0.077 199.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 19.111 1.256 4.521 0.003 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (381 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.5%. 96: The balanceable part of the MD step is 57%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.9%. 96: 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.095 0.048 199.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 30.920 0.776 2.794 0.004 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.2%. 96: The balanceable part of the MD step is 56%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.2%. 96: 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 114.032 0.210 0.758 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.6%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 198.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 118.926 0.202 0.727 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.6%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.017 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 84.290 0.285 1.025 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.7%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 100.502 0.239 0.860 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.2%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.6%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.014 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 102.903 0.233 0.840 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (201 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.6%. 96: The balanceable part of the MD step is 59%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.9%. 96: 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.045 0.023 198.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 65.197 0.368 1.325 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.9%. 96: The balanceable part of the MD step is 56%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.1%. 96: 96: 96: NOTE: 44 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.012 198.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 126.843 0.189 0.681 0.018 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.8%. 96: The balanceable part of the MD step is 51%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.9%. 96: 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 121.901 0.197 0.709 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.3%. 96: The balanceable part of the MD step is 50%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.016 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 93.892 0.256 0.920 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.1%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.6%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 99.610 0.241 0.867 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.2%. 96: The balanceable part of the MD step is 49%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.1%. 96: 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 90.382 0.266 0.956 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (175 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.046 0.023 199.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 63.908 0.376 1.352 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 44 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.018 0.009 197.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 160.857 0.149 0.537 0.022 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 198.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 115.859 0.207 0.746 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 90.162 0.266 0.958 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 90.650 0.265 0.953 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.038 0.019 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 76.728 0.313 1.126 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (179 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.044 0.022 199.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 66.800 0.359 1.293 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 198.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 119.255 0.201 0.724 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.012 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 124.363 0.193 0.695 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.016 198.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 93.847 0.256 0.921 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.034 0.017 198.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 84.508 0.284 1.022 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 88.655 0.271 0.975 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (179 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.043 0.022 199.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 67.322 0.356 1.283 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 198.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 115.686 0.207 0.747 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.022 0.011 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 133.472 0.180 0.647 0.019 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 198.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 88.750 0.270 0.974 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.036 0.018 198.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 81.471 0.295 1.060 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.015 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 95.027 0.253 0.909 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (181 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.046 0.023 199.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 63.602 0.377 1.358 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.014 198.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 106.779 0.225 0.809 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.014 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 106.725 0.225 0.810 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.018 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 83.737 0.287 1.032 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 98.332 0.244 0.879 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.018 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 83.386 0.288 1.036 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (186 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.055 0.028 199.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 53.245 0.451 1.623 0.007 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.014 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 105.506 0.227 0.819 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.020 0.010 197.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 143.684 0.167 0.601 0.020 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 88.311 0.272 0.978 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 198.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 111.058 0.216 0.778 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.022 0.011 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 131.668 0.182 0.656 0.018 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (176 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.037 0.019 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 77.916 0.308 1.109 0.011 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 43 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.008 197.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 173.114 0.139 0.499 0.024 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 42 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.006 196.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 254.738 0.094 0.339 0.035 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.020 0.010 197.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 148.362 0.162 0.582 0.021 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.020 0.010 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 145.469 0.165 0.594 0.020 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.020 0.010 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 148.013 0.162 0.584 0.021 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (147 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 87.939 0.273 0.983 0.012 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 43 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.018 0.009 197.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 160.990 0.149 0.537 0.022 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.009 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 167.110 0.144 0.517 0.023 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.009 197.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 172.556 0.139 0.501 0.024 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.012 197.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 124.274 0.193 0.695 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.024 0.012 198.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 119.354 0.201 0.724 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (151 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.039 0.019 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 75.709 0.317 1.141 0.011 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 40 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.011 0.006 195.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 260.265 0.092 0.332 0.036 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 44 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.007 196.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 198.473 0.121 0.435 0.028 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.021 0.011 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 135.105 0.178 0.640 0.019 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.008 196.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 189.080 0.127 0.457 0.026 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 96: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 96: 1 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.021 0.011 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 137.515 0.175 0.628 0.019 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (155 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 99.746 0.241 0.866 0.014 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 44 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.008 197.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 173.002 0.139 0.499 0.024 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.013 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 109.919 0.218 0.786 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 44 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.015 0.008 197.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 194.721 0.123 0.444 0.027 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.009 198.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 155.155 0.155 0.557 0.022 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.014 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 104.806 0.229 0.824 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (151 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 98.766 0.243 0.875 0.014 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 44 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.010 198.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 149.611 0.160 0.577 0.021 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 45 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.018 0.009 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 162.424 0.148 0.532 0.023 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.020 0.010 197.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 142.527 0.168 0.606 0.020 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.018 0.009 197.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 165.656 0.145 0.522 0.023 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.040 0.020 199.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 72.479 0.331 1.192 0.010 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (157 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.040 0.020 199.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 73.833 0.325 1.170 0.010 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 100.442 0.239 0.860 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 44 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.013 0.007 197.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 216.815 0.111 0.398 0.030 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 48 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 90.229 0.266 0.958 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.012 198.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 124.973 0.192 0.691 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 95.962 0.250 0.900 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (170 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.044 0.022 199.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 65.865 0.364 1.312 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 44 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.018 0.009 197.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 162.712 0.148 0.531 0.023 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 46 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.021 0.011 198.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 139.260 0.172 0.620 0.019 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 198.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 95.681 0.251 0.903 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 198.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 112.586 0.213 0.767 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: NOTE: 47 % of the run time was spent communicating energies, 96: you might want to increase some nst* mdp options 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.015 198.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 95.090 0.252 0.909 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (170 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.7%. 96: The balanceable part of the MD step is 62%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.1%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.039 0.020 197.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 75.298 0.319 1.147 0.010 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.2%. 96: The balanceable part of the MD step is 63%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.4%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.017 0.008 196.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 173.685 0.138 0.497 0.024 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 4. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 4. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.1%. 96: The balanceable part of the MD step is 55%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.2%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.018 0.009 195.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 160.409 0.150 0.539 0.022 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.0%. 96: The balanceable part of the MD step is 53%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.0%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.012 196.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 125.774 0.191 0.687 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.2%. 96: The balanceable part of the MD step is 52%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.1%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.034 0.017 197.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 85.244 0.282 1.014 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 100. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 100. 96: 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.4%. 96: The balanceable part of the MD step is 54%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.3%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 197.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 100.567 0.239 0.859 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (164 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.5%. 96: The balanceable part of the MD step is 63%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.9%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.045 0.023 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 64.091 0.374 1.348 0.009 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.7%. 96: The balanceable part of the MD step is 64%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.1%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.012 197.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 123.475 0.194 0.700 0.017 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.7%. 96: The balanceable part of the MD step is 59%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.0%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 197.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 117.045 0.205 0.738 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.3%. 96: The balanceable part of the MD step is 57%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.014 197.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 107.447 0.223 0.804 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.5%. 96: The balanceable part of the MD step is 54%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.012 196.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 126.648 0.190 0.682 0.018 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.4%. 96: The balanceable part of the MD step is 57%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.8%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.021 0.011 196.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 135.982 0.176 0.635 0.019 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (166 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.5%. 96: The balanceable part of the MD step is 63%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.9%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.055 0.028 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 52.964 0.453 1.631 0.007 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 2.1%. 96: The balanceable part of the MD step is 63%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.3%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.014 197.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 103.313 0.232 0.836 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.7%. 96: The balanceable part of the MD step is 58%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 1.0%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.021 0.011 196.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 135.886 0.177 0.636 0.019 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.2%. 96: The balanceable part of the MD step is 57%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.7%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.025 0.013 196.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 113.610 0.211 0.760 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 0.9%. 96: The balanceable part of the MD step is 59%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.5%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 196.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 109.887 0.218 0.786 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 96: NVE simulation: will use the initial temperature of 68.810 K for 96: determining the Verlet buffer size 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Can not increase nstlist because an NVE ensemble is used 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: 96: Dynamic load balancing report: 96: DLB was off during the run due to low measured imbalance. 96: Average load imbalance: 1.5%. 96: The balanceable part of the MD step is 57%, load imbalance is computed from this. 96: Part of the total run time spent waiting due to load imbalance: 0.9%. 96: 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 197.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 111.078 0.216 0.778 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (179 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.052 0.026 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 55.716 0.431 1.551 0.008 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 196.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 110.432 0.217 0.782 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.014 197.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 105.056 0.228 0.822 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 196.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 109.698 0.219 0.788 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 197.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 91.614 0.262 0.943 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.014 196.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 101.553 0.236 0.851 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (181 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.052 0.026 198.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 56.416 0.425 1.531 0.008 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 197.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 98.466 0.244 0.877 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.014 196.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 105.787 0.227 0.817 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 197.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 90.493 0.265 0.955 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 196.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 112.046 0.214 0.771 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 96: The Berendsen barostat does not generate any strictly correct ensemble, 96: and should not be used for new production simulations (in our opinion). 96: We recommend using the C-rescale barostat instead. 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: 96: There was 1 WARNING 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.034 0.017 197.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 84.863 0.283 1.018 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (184 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.035 0.018 197.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 83.300 0.288 1.037 0.012 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.019 0.010 195.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 151.711 0.158 0.570 0.021 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.023 0.012 196.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 126.111 0.190 0.685 0.018 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.027 0.014 196.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 105.859 0.227 0.816 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.033 0.017 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 87.457 0.274 0.988 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.016 197.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 93.833 0.256 0.921 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (168 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 197.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 91.107 0.263 0.948 0.013 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.068 0.034 198.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 42.676 0.562 2.025 0.006 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 196.8 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 111.810 0.215 0.773 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.040 0.020 198.0 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 72.607 0.331 1.190 0.010 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.032 0.016 197.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 90.789 0.264 0.952 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 2 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.053 0.027 198.5 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 55.063 0.436 1.569 0.008 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (209 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.051 0.026 198.3 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 57.420 0.418 1.505 0.008 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There were 3 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.036 0.018 197.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 80.575 0.298 1.072 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 196.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 109.058 0.220 0.792 0.015 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.028 0.014 196.7 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 102.875 0.233 0.840 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.026 0.013 196.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 112.350 0.214 0.769 0.016 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: 96: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: MTTK coupling is deprecated and will soon be removed 96: 96: 96: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: for current Trotter decomposition methods with vv, nsttcouple and 96: nstpcouple must be equal. Both have been reset to 96: min(nsttcouple,nstpcouple) = 2 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 96: COM removal frequency is set to (5). 96: Other settings require a global communication frequency of 2. 96: Note that this will require additional global communication steps, 96: which will reduce performance when using multiple ranks. 96: Consider setting nstcomm to a multiple of 2. 96: 96: 96: There were 4 NOTEs 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.038 0.019 197.6 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 77.149 0.311 1.120 0.011 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (187 ms) 96: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.040 0.020 198.1 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 72.184 0.332 1.197 0.010 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (1) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.030 0.015 197.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 96.956 0.248 0.891 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: Setting nstcalcenergy (100) equal to nstenergy (4) 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.018 0.009 195.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 157.236 0.153 0.549 0.022 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.034 0.017 197.2 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 86.215 0.278 1.002 0.012 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.031 0.016 197.4 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 92.674 0.259 0.932 0.013 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: 96: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 96: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 96: setting nstcomm equal to nstcalcenergy for less overhead 96: 96: Number of degrees of freedom in T-Coupling group System is 33.00 96: 96: There was 1 NOTE 96: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 96: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 96: 96: Using 2 MPI threads 96: Using 1 OpenMP thread per tMPI thread 96: 96: 96: NOTE: The number of threads is not equal to the number of (logical) cpus 96: and the -pin option is set to auto: will not pin threads to cpus. 96: This can lead to significant performance degradation. 96: Consider using -pin on (and -pinoffset in case you run multiple jobs). 96: starting mdrun 'Argon' 96: 16 steps, 0.0 ps. 96: Generated 1 of the 1 non-bonded parameter combinations 96: 96: Excluding 1 bonded neighbours molecule type 'Argon' 96: 96: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 96: 96: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 96: 96: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 96: 96: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 96: 96: Note that mdrun will redetermine rlist based on the actual pair-list setup 96: 96: This run will generate roughly 0 Mb of data 96: 96: Writing final coordinates. 96: 96: Core t (s) Wall t (s) (%) 96: Time: 0.029 0.015 196.9 96: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 96: Performance: 100.150 0.240 0.863 0.014 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 96: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 96: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (176 ms) 96: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (5598 ms total) 96: 96: [----------] Global test environment tear-down 96: [==========] 25 tests from 1 test suite ran. (5614 ms total) 96: [ PASSED ] 25 tests. 96/103 Test #96: MdrunCoordinationCouplingTests2Ranks ...... Passed 5.64 sec test 97 Start 97: MdrunCoordinationConstraintsTests1Rank 97: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 97: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 97: Test timeout computed to be: 1920 97: [==========] Running 13 tests from 1 test suite. 97: [----------] Global test environment set-up. 97: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.055 0.055 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 26.773 0.896 3.227 0.005 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.048 0.048 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 30.573 0.785 2.826 0.005 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.296 0.680 2.448 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.265 0.700 2.522 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.347 0.699 2.515 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.118 0.703 2.532 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (6243 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.177 0.723 2.604 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.738 0.691 2.487 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.114 0.683 2.461 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.234 0.701 2.524 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.242 0.701 2.523 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.460 0.696 2.507 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (6203 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.574 0.715 2.573 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.074 0.684 2.463 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.062 0.062 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 23.611 1.016 3.659 0.004 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.424 0.697 2.510 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.797 0.732 2.634 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.168 0.724 2.605 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (6309 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.180 0.723 2.604 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 35.013 0.685 2.468 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.862 0.688 2.478 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.642 0.713 2.568 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.725 0.712 2.562 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.399 0.719 2.587 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (6260 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.905 0.729 2.626 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.765 0.690 2.485 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.811 0.689 2.482 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.856 0.709 2.552 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.748 0.711 2.560 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.707 0.712 2.563 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (6222 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.7 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.343 0.720 2.591 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.733 0.691 2.488 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.210 0.702 2.526 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.826 0.710 2.554 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.770 0.711 2.558 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.566 0.715 2.574 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (6249 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.016 0.727 2.617 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.791 0.690 2.483 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.578 0.694 2.499 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.718 0.712 2.562 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.592 0.714 2.572 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.622 0.714 2.570 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (6274 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.442 0.718 2.584 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.443 0.697 2.508 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.451 0.697 2.508 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.615 0.714 2.570 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.616 0.714 2.570 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.467 0.717 2.582 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (6292 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.088 0.725 2.611 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.042 0.042 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.665 0.692 2.492 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.052 0.052 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 28.097 0.854 3.075 0.005 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.504 0.716 2.579 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.592 0.714 2.572 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.444 0.718 2.583 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (6298 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.623 0.736 2.648 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.136 0.703 2.531 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 4. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 4. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.232 0.701 2.524 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.045 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.978 0.728 2.620 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.361 0.719 2.590 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 100. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 100. 97: 97: 97: There were 4 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.313 0.720 2.594 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (6282 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.546 0.737 2.655 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.063 0.705 2.536 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.365 0.698 2.514 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.874 0.730 2.628 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.812 0.731 2.633 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: NVE simulation: will use the initial temperature of 398.997 K for 97: determining the Verlet buffer size 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Can not increase nstlist because an NVE ensemble is used 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.9 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.954 0.728 2.622 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (6277 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.046 0.046 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.189 0.746 2.684 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.819 0.731 2.633 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.043 0.043 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 34.164 0.702 2.529 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.147 0.724 2.607 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.640 0.713 2.568 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 97: COM removal frequency is set to (5). 97: Other settings require a global communication frequency of 2. 97: Note that this will require additional global communication steps, 97: which will reduce performance when using multiple ranks. 97: Consider setting nstcomm to a multiple of 2. 97: 97: 97: There were 3 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.137 0.724 2.607 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (6278 ms) 97: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.305 0.743 2.674 0.006 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (1) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.607 0.714 2.571 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: Setting nstcalcenergy (100) equal to nstenergy (4) 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.498 0.716 2.579 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.012 0.012 99.2 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 119.707 0.200 0.722 0.021 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.045 0.045 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 32.841 0.731 2.631 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: 97: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 97: setting nstcomm equal to nstcalcenergy for less overhead 97: 97: Generating 1-4 interactions: fudge = 0.5 97: Number of degrees of freedom in T-Coupling group System is 27.00 97: 97: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 97: You are using a plain Coulomb cut-off, which might produce artifacts. 97: You might want to consider using PME electrostatics. 97: 97: 97: 97: There were 2 NOTEs 97: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 97: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 97: 97: Using 1 MPI thread 97: Using 1 OpenMP thread 97: 97: 97: NOTE: Thread affinity was not set. 97: starting mdrun 'spc2' 97: 16 steps, 0.0 ps. 97: Generated 330891 of the 330891 non-bonded parameter combinations 97: 97: Generated 330891 of the 330891 1-4 parameter combinations 97: 97: Excluding 2 bonded neighbours molecule type 'SOL' 97: 97: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 97: 97: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 97: 97: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 97: 97: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 97: 97: Note that mdrun will redetermine rlist based on the actual pair-list setup 97: 97: This run will generate roughly 0 Mb of data 97: 97: Writing final coordinates. 97: 97: Core t (s) Wall t (s) (%) 97: Time: 0.044 0.044 99.8 97: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 97: Performance: 33.150 0.724 2.606 0.006 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 97: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 97: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (6276 ms) 97: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (81471 ms total) 97: 97: [----------] Global test environment tear-down 97: [==========] 13 tests from 1 test suite ran. (81487 ms total) 97: [ PASSED ] 13 tests. 97/103 Test #97: MdrunCoordinationConstraintsTests1Rank .... Passed 81.53 sec test 98 Start 98: MdrunCoordinationConstraintsTests2Ranks 98: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 98: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 98: Test timeout computed to be: 1920 98: [==========] Running 13 tests from 1 test suite. 98: [----------] Global test environment set-up. 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 3.6%. 98: The balanceable part of the MD step is 57%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.0%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.646 0.735 2.647 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.6%. 98: The balanceable part of the MD step is 53%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.0%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.347 0.699 2.515 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 7.2%. 98: The balanceable part of the MD step is 46%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.3%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.896 0.730 2.626 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 7.1%. 98: The balanceable part of the MD step is 43%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.1%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.768 0.711 2.559 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 7.1%. 98: The balanceable part of the MD step is 45%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.2%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.307 0.721 2.594 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 7.7%. 98: The balanceable part of the MD step is 44%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.4%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.092 0.046 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.924 0.752 2.706 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (6461 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 3.6%. 98: The balanceable part of the MD step is 56%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.0%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.618 0.736 2.649 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.5%. 98: The balanceable part of the MD step is 53%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.9%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.311 0.699 2.518 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 6.7%. 98: The balanceable part of the MD step is 49%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.3%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.083 0.042 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 35.085 0.684 2.463 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.8%. 98: The balanceable part of the MD step is 48%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.8%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.898 0.730 2.626 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.4%. 98: The balanceable part of the MD step is 47%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.5%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.485 0.717 2.580 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.9%. 98: The balanceable part of the MD step is 48%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.8%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.040 0.705 2.538 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (6476 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 3.7%. 98: The balanceable part of the MD step is 57%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.1%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.547 0.737 2.655 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.2%. 98: The balanceable part of the MD step is 55%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.8%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.559 0.694 2.500 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 6.3%. 98: The balanceable part of the MD step is 49%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.1%. 98: 98: 98: NOTE: 48 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.059 0.030 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 49.578 0.484 1.743 0.009 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 6.3%. 98: The balanceable part of the MD step is 48%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.0%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.583 0.715 2.573 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 6.0%. 98: The balanceable part of the MD step is 48%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.9%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.320 0.720 2.593 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.8%. 98: The balanceable part of the MD step is 48%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.8%. 98: 98: 98: NOTE: 49 % of the run time was spent communicating energies, 98: you might want to increase some nst* mdp options 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.321 0.720 2.593 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (6450 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.721 0.733 2.640 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.188 0.702 2.527 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.084 0.042 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.809 0.689 2.482 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.669 0.713 2.566 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.352 0.720 2.591 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.389 0.719 2.588 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (6495 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.736 0.733 2.639 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.078 0.704 2.535 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.862 0.709 2.552 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.217 0.723 2.601 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.994 0.727 2.619 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.536 0.716 2.576 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (6513 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.094 0.047 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.017 0.774 2.786 0.005 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.167 0.702 2.529 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.042 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.663 0.692 2.493 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.535 0.716 2.576 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.549 0.715 2.575 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.523 0.716 2.577 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (6485 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.719 0.734 2.641 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.122 0.703 2.532 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.042 199.4 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.637 0.693 2.494 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.096 0.048 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 30.427 0.789 2.840 0.005 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.435 0.718 2.584 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.295 0.700 2.519 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (6453 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.951 0.728 2.622 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.188 0.702 2.527 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.461 0.696 2.507 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.087 0.725 2.611 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.564 0.715 2.574 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.086 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.941 0.707 2.546 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (6499 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.939 0.729 2.623 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.464 0.696 2.507 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.085 0.043 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 34.529 0.695 2.502 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.345 0.720 2.591 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.388 0.719 2.588 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.489 0.717 2.580 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (6519 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 3.3%. 98: The balanceable part of the MD step is 61%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.0%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.079 0.040 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 36.810 0.652 2.347 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.2%. 98: The balanceable part of the MD step is 61%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.2%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.506 0.716 2.579 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 4. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 4. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 6.5%. 98: The balanceable part of the MD step is 55%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.6%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.722 0.712 2.562 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.8%. 98: The balanceable part of the MD step is 54%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.1%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.2 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.582 0.737 2.652 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.4%. 98: The balanceable part of the MD step is 53%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.9%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.256 0.722 2.598 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 100. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 100. 98: 98: 98: There were 4 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.6%. 98: The balanceable part of the MD step is 54%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.0%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.785 0.732 2.635 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (6481 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 3.4%. 98: The balanceable part of the MD step is 62%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.1%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.092 0.046 199.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.896 0.752 2.709 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.1%. 98: The balanceable part of the MD step is 61%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 3.1%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 198.3 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.765 0.732 2.637 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.4%. 98: The balanceable part of the MD step is 52%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.8%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.694 0.734 2.643 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 4.9%. 98: The balanceable part of the MD step is 56%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.8%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.370 0.741 2.669 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 5.0%. 98: The balanceable part of the MD step is 57%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.9%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.093 0.047 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.389 0.765 2.753 0.005 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: NVE simulation: will use the initial temperature of 398.997 K for 98: determining the Verlet buffer size 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Can not increase nstlist because an NVE ensemble is used 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: 98: Dynamic load balancing report: 98: DLB got disabled because it was unsuitable to use. 98: Average load imbalance: 4.2%. 98: The balanceable part of the MD step is 57%, load imbalance is computed from this. 98: Part of the total run time spent waiting due to load imbalance: 2.4%. 98: 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.618 0.736 2.649 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (6514 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.091 0.046 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.958 0.751 2.704 0.006 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 198.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.595 0.714 2.572 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 198.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.473 0.717 2.581 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.537 0.738 2.655 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.089 0.045 198.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.777 0.732 2.636 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 98: COM removal frequency is set to (5). 98: Other settings require a global communication frequency of 2. 98: Note that this will require additional global communication steps, 98: which will reduce performance when using multiple ranks. 98: Consider setting nstcomm to a multiple of 2. 98: 98: 98: There were 3 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 199.0 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.491 0.739 2.659 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (6497 ms) 98: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.093 0.046 198.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 31.588 0.760 2.735 0.005 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (1) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.088 0.044 198.8 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.125 0.725 2.608 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: Setting nstcalcenergy (100) equal to nstenergy (4) 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.087 0.044 198.7 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 33.490 0.717 2.580 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.090 0.045 198.9 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.481 0.739 2.660 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.091 0.046 198.5 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 32.082 0.748 2.693 0.006 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: 98: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 98: setting nstcomm equal to nstcalcenergy for less overhead 98: 98: Generating 1-4 interactions: fudge = 0.5 98: Number of degrees of freedom in T-Coupling group System is 27.00 98: 98: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 98: You are using a plain Coulomb cut-off, which might produce artifacts. 98: You might want to consider using PME electrostatics. 98: 98: 98: 98: There were 2 NOTEs 98: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 98: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 98: 98: Using 2 MPI threads 98: Using 1 OpenMP thread per tMPI thread 98: 98: 98: NOTE: The number of threads is not equal to the number of (logical) cpus 98: and the -pin option is set to auto: will not pin threads to cpus. 98: This can lead to significant performance degradation. 98: Consider using -pin on (and -pinoffset in case you run multiple jobs). 98: starting mdrun 'spc2' 98: 16 steps, 0.0 ps. 98: Generated 330891 of the 330891 non-bonded parameter combinations 98: 98: Generated 330891 of the 330891 1-4 parameter combinations 98: 98: Excluding 2 bonded neighbours molecule type 'SOL' 98: 98: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 98: 98: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 98: 98: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 98: 98: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 98: 98: Note that mdrun will redetermine rlist based on the actual pair-list setup 98: 98: This run will generate roughly 0 Mb of data 98: 98: Writing final coordinates. 98: 98: Core t (s) Wall t (s) (%) 98: Time: 0.095 0.047 199.1 98: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 98: Performance: 30.925 0.776 2.794 0.005 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 98: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 98: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (6500 ms) 98: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (84350 ms total) 98: 98: [----------] Global test environment tear-down 98: [==========] 13 tests from 1 test suite ran. (84366 ms total) 98: [ PASSED ] 13 tests. 98/103 Test #98: MdrunCoordinationConstraintsTests2Ranks ... Passed 84.40 sec test 99 Start 99: MdrunFEPTests 99: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" 99: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 99: Test timeout computed to be: 600 99: [==========] Running 14 tests from 2 test suites. 99: [----------] Global test environment set-up. 99: [----------] 2 tests from ExpandedEnsembleTest 99: [ RUN ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 79.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There was 1 NOTE 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun '30 atom system in water' 99: 16 steps, 0.0 ps. 99: Generated 2485 of the 2485 non-bonded parameter combinations 99: 99: Generated 2485 of the 2485 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'nonanol' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.170 0.085 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 17.283 1.389 4.999 0.007 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_ContinuationPreservesExpandedEnsembleState.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Overriding nsteps with value passed on the command line: 8 steps, 0.008 ps 99: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 99: 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun '30 atom system in water' 99: 24 steps, 0.0 ps (continuing from step 16, 0.0 ps). 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.026 0.013 196.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 59.473 0.404 1.453 0.025 99: [ OK ] ExpandedEnsembleTest.ContinuationPreservesExpandedEnsembleState (194 ms) 99: [ RUN ] ExpandedEnsembleTest.WeightEquilibrationReported 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 79.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported_input.mdp]: 99: You are using a plain Coulomb cut-off, which might produce artifacts. 99: You might want to consider using PME electrostatics. 99: 99: 99: 99: There was 1 NOTE 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsembleTest_WeightEquilibrationReported.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun '30 atom system in water' 99: 1 steps, 0.0 ps. 99: Generated 2485 of the 2485 non-bonded parameter combinations 99: 99: Generated 2485 of the 2485 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'nonanol' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/nonanol_vacuo.gro' 99: 99: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.020 0.010 198.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 17.162 1.398 5.034 0.007 99: [ OK ] ExpandedEnsembleTest.WeightEquilibrationReported (63 ms) 99: [----------] 2 tests from ExpandedEnsembleTest (258 ms total) 99: 99: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 3 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to 1728039663 99: 99: Generated 153 of the 153 non-bonded parameter combinations 99: 99: Generated 153 of the 153 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'ASN' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.291 0.145 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 12.475 1.924 6.926 0.026 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) 99: 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (459 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 3 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to 1946155005 99: 99: Generated 153 of the 153 non-bonded parameter combinations 99: 99: Generated 153 of the 153 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'ASN' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.290 0.145 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 12.517 1.917 6.902 0.026 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (449 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 99: With PME there is a minor soft core effect present at the cut-off, 99: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 99: energy conservation, but usually other effects dominate. With a common 99: sigma value of 0.34 nm the fraction of the particle-particle potential at 99: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 4 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to 131850106 99: 99: Generated 153 of the 153 non-bonded parameter combinations 99: 99: Generated 153 of the 153 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'ASN' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.227 0.114 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 15.981 1.502 5.407 0.033 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (417 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 99: With PME there is a minor soft core effect present at the cut-off, 99: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 99: energy conservation, but usually other effects dominate. With a common 99: sigma value of 0.34 nm the fraction of the particle-particle potential at 99: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: 99: NOTE 3 [file topol.top, line 155]: 99: System has non-zero total charge: 1.000000 99: Total charge should normally be an integer. See 99: https://manual.gromacs.org/current/user-guide/floating-point.html 99: for discussion on how close it should be to an integer. 99: 99: 99: 99: 99: WARNING 2 [file topol.top, line 155]: 99: You are using Ewald electrostatics in a system with net charge. This can 99: lead to severe artifacts, such as ions moving into regions with low 99: dielectric, due to the uniform background charge. We suggest to 99: neutralize your system with counter ions, possibly in combination with a 99: physiological salt concentration. 99: 99: Setting the LD random seed to -1141962849 99: 99: Generated 171 of the 171 non-bonded parameter combinations 99: 99: Generated 171 of the 171 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Excluding 1 bonded neighbours molecule type 'NA' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'ASN' 99: 99: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 99: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 99: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 99: Charge 99: J. Chem. Theory Comput. (2014) 99: https://doi.org/10.1021/ct400626b 99: -------- -------- --- Thank You --- -------- -------- 99: 99: Number of degrees of freedom in T-Coupling group System is 358.00 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 5 NOTEs 99: 99: There were 2 WARNINGs 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: There are: 1 Ion residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 99: 99: Estimate for the relative computational load of the PME mesh part: 0.92 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.262 0.131 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 13.818 1.737 6.253 0.028 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d (198 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 99: With PME there is a minor soft core effect present at the cut-off, 99: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 99: energy conservation, but usually other effects dominate. With a common 99: sigma value of 0.34 nm the fraction of the particle-particle potential at 99: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: 99: NOTE 3 [file topol.top, line 165]: 99: System has non-zero total charge: 1.000000 99: Total charge should normally be an integer. See 99: https://manual.gromacs.org/current/user-guide/floating-point.html 99: for discussion on how close it should be to an integer. 99: 99: 99: 99: 99: WARNING 2 [file topol.top, line 165]: 99: You are using Ewald electrostatics in a system with net charge. This can 99: lead to severe artifacts, such as ions moving into regions with low 99: dielectric, due to the uniform background charge. We suggest to 99: neutralize your system with counter ions, possibly in combination with a 99: physiological salt concentration. 99: 99: Setting the LD random seed to 2076114939 99: 99: Generated 190 of the 190 non-bonded parameter combinations 99: 99: Generated 190 of the 190 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Excluding 1 bonded neighbours molecule type 'NA' 99: 99: turning H bonds into constraints... 99: 99: Excluding 1 bonded neighbours molecule type 'CL' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'CL' 99: 99: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 99: J. S. Hub, B. L. de Groot, H. Grubmüller, G. Groenhof 99: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 99: Charge 99: J. Chem. Theory Comput. (2014) 99: https://doi.org/10.1021/ct400626b 99: -------- -------- --- Thank You --- -------- -------- 99: 99: Number of degrees of freedom in T-Coupling group System is 361.00 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 5 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 5 NOTEs 99: 99: There were 2 WARNINGs 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: There are: 2 Ion residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 99: 99: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 99: 99: Estimate for the relative computational load of the PME mesh part: 0.92 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.300 0.150 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 12.100 1.984 7.141 0.025 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d (212 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 99: For proper sampling of the (nearly) decoupled state, stochastic dynamics 99: should be used 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 99: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 99: and vdw_modifier=Force-switch 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 4 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 100 steps, 0.1 ps. 99: Setting the LD random seed to -992231989 99: 99: Generated 153 of the 153 non-bonded parameter combinations 99: 99: Generated 153 of the 153 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Coupling 1 copies of molecule type 'ASN' 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/expanded/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 1.088 0.544 200.0 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 16.034 1.497 5.389 0.033 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (856 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: 99: WARNING 2 [file topol.top, line 72]: 99: No default Bond types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '7 8 1'. 99: 99: 99: WARNING 3 [file topol.top, line 73]: 99: No default Bond types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '7 9 1'. 99: 99: 99: WARNING 4 [file topol.top, line 98]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '6 5 7 1'. 99: 99: 99: WARNING 5 [file topol.top, line 99]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '5 7 8 1'. 99: 99: 99: WARNING 6 [file topol.top, line 100]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '5 7 9 1'. 99: 99: 99: WARNING 7 [file topol.top, line 101]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '8 7 9 1'. 99: 99: 99: WARNING 8 [file topol.top, line 111]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '1 5 7 8 3'. 99: 99: 99: WARNING 9 [file topol.top, line 112]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '1 5 7 9 3'. 99: 99: 99: WARNING 10 [file topol.top, line 113]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '6 5 7 8 3'. 99: 99: 99: WARNING 11 [file topol.top, line 114]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '6 5 7 9 3'. 99: 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 2 NOTEs 99: 99: There were 11 WARNINGs 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to 1056794743 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.460 0.230 199.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 7.888 3.043 10.954 0.016 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (533 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: 99: WARNING 2 [file topol.top, line 72]: 99: No default Bond types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '7 8 1'. 99: 99: 99: WARNING 3 [file topol.top, line 73]: 99: No default Bond types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '7 9 1'. 99: 99: 99: WARNING 4 [file topol.top, line 98]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '6 5 7 1'. 99: 99: 99: WARNING 5 [file topol.top, line 99]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '5 7 8 1'. 99: 99: 99: WARNING 6 [file topol.top, line 100]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '5 7 9 1'. 99: 99: 99: WARNING 7 [file topol.top, line 101]: 99: No default Angle types for perturbed atoms in interaction, using normal 99: values. The interaction was 99: '8 7 9 1'. 99: 99: 99: WARNING 8 [file topol.top, line 111]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '1 5 7 8 3'. 99: 99: 99: WARNING 9 [file topol.top, line 112]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '1 5 7 9 3'. 99: 99: 99: WARNING 10 [file topol.top, line 113]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '6 5 7 8 3'. 99: 99: 99: WARNING 11 [file topol.top, line 114]: 99: No default Ryckaert-Bell. types for perturbed atoms in interaction, using 99: normal values. The interaction was 99: '6 5 7 9 3'. 99: 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 99: Removing center of mass motion in the presence of position restraints 99: might cause artifacts. When you are using position restraints to 99: equilibrate a macro-molecule, the artifacts are usually negligible. 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 3 NOTEs 99: 99: There were 11 WARNINGs 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to 2131357679 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.461 0.231 199.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 7.864 3.052 10.987 0.016 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (534 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 2 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to -38029570 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/restraints/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.81 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.165 0.082 199.7 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 21.997 1.091 3.928 0.045 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (385 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: There was 1 NOTE 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.078 0.039 199.3 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 46.322 0.518 1.865 0.095 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 99: Setting the LD random seed to -807424049 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/simtemp/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.81 99: 99: This run will generate roughly 0 Mb of data 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (376 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 99: With PME there is a minor soft core effect present at the cut-off, 99: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 99: energy conservation, but usually other effects dominate. With a common 99: sigma value of 0.34 nm the fraction of the particle-particle potential at 99: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 3 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to -1090551830 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/transformAtoB/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.89 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.283 0.142 199.9 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 12.796 1.876 6.752 0.026 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (443 ms) 99: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d 99: 99: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 99: With PME there is a minor soft core effect present at the cut-off, 99: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 99: energy conservation, but usually other effects dominate. With a common 99: sigma value of 0.34 nm the fraction of the particle-particle potential at 99: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 99: 99: 99: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 99: The Berendsen thermostat does not generate the correct kinetic energy 99: distribution, and should not be used for new production simulations (in 99: our opinion). We would recommend the V-rescale thermostat. 99: 99: Generating 1-4 interactions: fudge = 0.5 99: Number of degrees of freedom in T-Coupling group System is 355.00 99: 99: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 99: The optimal PME mesh load for parallel simulations is below 0.5 99: and for highly parallel simulations between 0.25 and 0.33, 99: for higher performance, increase the cut-off and the PME grid spacing. 99: 99: 99: 99: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 99: For free energy simulations, the optimal load limit increases from 0.5 to 99: 0.667 99: 99: 99: 99: There were 3 NOTEs 99: 99: There was 1 WARNING 99: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 99: Changing nstlist from 10 to 100, rlist from 1 to 1 99: 99: Using 1 MPI thread 99: Using 2 OpenMP threads 99: 99: 99: NOTE: The number of threads is not equal to the number of (logical) cpus 99: and the -pin option is set to auto: will not pin threads to cpus. 99: This can lead to significant performance degradation. 99: Consider using -pin on (and -pinoffset in case you run multiple jobs). 99: starting mdrun 'AA' 99: 20 steps, 0.0 ps. 99: Setting the LD random seed to -338176130 99: 99: Generated 136 of the 136 non-bonded parameter combinations 99: 99: Generated 136 of the 136 1-4 parameter combinations 99: 99: Excluding 3 bonded neighbours molecule type 'ASN' 99: 99: turning H bonds into constraints... 99: 99: Excluding 2 bonded neighbours molecule type 'SOL' 99: 99: turning H bonds into constraints... 99: 99: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/freeenergy/vdwalone/conf.gro' 99: Analysing residue names: 99: There are: 1 Protein residues 99: There are: 56 Water residues 99: Analysing Protein... 99: 99: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 99: 99: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 99: 99: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 99: 99: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 99: 99: Note that mdrun will redetermine rlist based on the actual pair-list setup 99: Calculating fourier grid dimensions for X Y Z 99: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 99: 99: Estimate for the relative computational load of the PME mesh part: 0.81 99: 99: This run will generate roughly 0 Mb of data 99: 99: Writing final coordinates. 99: 99: Core t (s) Wall t (s) (%) 99: Time: 0.174 0.087 199.8 99: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 99: Performance: 20.800 1.154 4.154 0.043 99: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file 99: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 99: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (390 ms) 99: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (5272 ms total) 99: 99: [----------] Global test environment tear-down 99: [==========] 14 tests from 2 test suites ran. (5563 ms total) 99: [ PASSED ] 14 tests. 99/103 Test #99: MdrunFEPTests ............................. Passed 5.59 sec test 100 Start 100: MdrunPullTests 100: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" 100: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 100: Test timeout computed to be: 600 100: [==========] Running 4 tests from 1 test suite. 100: [----------] Global test environment set-up. 100: [----------] 4 tests from PullTest/PullIntegrationTest 100: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 100: Generating 1-4 interactions: fudge = 0.5 100: Pull group 1 'r_1' has 3 atoms 100: Pull group 2 'r_2' has 3 atoms 100: Number of degrees of freedom in T-Coupling group System is 1293.00 100: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 100: NVE simulation: will use the initial temperature of 303.122 K for 100: determining the Verlet buffer size 100: 100: Pull group natoms pbc atom distance at start reference at t=0 100: 1 3 2 100: 2 3 5 0.575 nm 0.600 nm 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 100: Can not increase nstlist because an NVE ensemble is used 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'spc2' 100: 20 steps, 0.0 ps. 100: Generated 330891 of the 330891 non-bonded parameter combinations 100: 100: Generated 330891 of the 330891 1-4 parameter combinations 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.194 0.097 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 18.731 1.281 4.613 0.140 100: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (1108 ms) 100: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 100: Generating 1-4 interactions: fudge = 0.5 100: Pull group 1 'r_1' has 3 atoms 100: Pull group 2 'r_2' has 3 atoms 100: Number of degrees of freedom in T-Coupling group System is 1293.00 100: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 100: NVE simulation: will use the initial temperature of 303.122 K for 100: determining the Verlet buffer size 100: 100: Pull group natoms pbc atom distance at start reference at t=0 100: 1 3 2 100: 2 3 5 0.301 nm 0.400 nm 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 100: Can not increase nstlist because an NVE ensemble is used 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'spc2' 100: 20 steps, 0.0 ps. 100: Generated 330891 of the 330891 non-bonded parameter combinations 100: 100: Generated 330891 of the 330891 1-4 parameter combinations 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.253 0.126 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 14.350 1.672 6.021 0.108 100: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (1151 ms) 100: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 100: Generating 1-4 interactions: fudge = 0.5 100: Pull group 1 'r_1' has 3 atoms 100: Pull group 2 'r_2' has 3 atoms 100: Pull group 3 'r_3' has 3 atoms 100: Number of degrees of freedom in T-Coupling group System is 1292.00 100: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 100: NVE simulation: will use the initial temperature of 303.357 K for 100: determining the Verlet buffer size 100: 100: Pull group natoms pbc atom distance at start reference at t=0 100: 1 3 2 100: 2 3 5 0.575 nm 0.500 nm 100: 1 3 2 100: 3 3 8 0.331 nm 0.400 nm 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 100: Can not increase nstlist because an NVE ensemble is used 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'spc2' 100: 20 steps, 0.0 ps. 100: Generated 330891 of the 330891 non-bonded parameter combinations 100: 100: Generated 330891 of the 330891 1-4 parameter combinations 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.253 0.127 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 14.303 1.678 6.041 0.107 100: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (1145 ms) 100: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 100: Generating 1-4 interactions: fudge = 0.5 100: Pull group 1 'r_1' has 3 atoms 100: Pull group 2 'r_2' has 3 atoms 100: Number of degrees of freedom in T-Coupling group System is 1293.00 100: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 100: 100: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 100: NVE simulation: will use the initial temperature of 303.122 K for 100: determining the Verlet buffer size 100: 100: Pull group natoms pbc atom distance at start reference at t=0 100: 1 3 2 100: 2 3 5 0.575 nm 0.000 nm 100: 0.050 nm 0.000 nm 100: 100: There was 1 NOTE 100: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 100: Can not increase nstlist because an NVE ensemble is used 100: Using 1 MPI thread 100: Using 2 OpenMP threads 100: 100: 100: NOTE: The number of threads is not equal to the number of (logical) cpus 100: and the -pin option is set to auto: will not pin threads to cpus. 100: This can lead to significant performance degradation. 100: Consider using -pin on (and -pinoffset in case you run multiple jobs). 100: starting mdrun 'spc2' 100: 20 steps, 0.0 ps. 100: Generated 330891 of the 330891 non-bonded parameter combinations 100: 100: Generated 330891 of the 330891 1-4 parameter combinations 100: 100: Excluding 2 bonded neighbours molecule type 'SOL' 100: 100: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc216.gro' 100: 100: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 100: 100: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 100: 100: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 100: 100: Note that mdrun will redetermine rlist based on the actual pair-list setup 100: 100: This run will generate roughly 0 Mb of data 100: 100: Writing final coordinates. 100: 100: Core t (s) Wall t (s) (%) 100: Time: 0.252 0.126 199.8 100: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 100: Performance: 14.371 1.670 6.012 0.108 100: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file 100: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (1150 ms) 100: [----------] 4 tests from PullTest/PullIntegrationTest (4556 ms total) 100: 100: [----------] Global test environment tear-down 100: [==========] 4 tests from 1 test suite ran. (4572 ms total) 100: [ PASSED ] 4 tests. 100/103 Test #100: MdrunPullTests ............................ Passed 4.61 sec test 101 Start 101: MdrunRotationTests 101: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunRotationTests.xml" 101: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 101: Test timeout computed to be: 600 101: [==========] Running 12 tests from 1 test suite. 101: [----------] Global test environment set-up. 101: [----------] 12 tests from RotationWorks/RotationTest 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 101: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: trr version: GMX_trn_file (single precision) 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to 1543237567 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.020 0.010 198.1 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 452.637 0.053 0.382 0.010 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (30 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 101: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -67313729 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.017 0.009 197.9 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 509.798 0.047 0.339 0.012 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (27 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 101: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -553675410 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.040 0.020 199.1 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 223.691 0.107 0.772 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (38 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 101: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -16154702 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.044 0.022 199.2 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 202.306 0.119 0.854 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (39 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 101: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -536870913 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.043 0.022 199.2 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 207.061 0.116 0.835 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (38 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 101: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -1074021415 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.045 0.023 199.2 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 198.690 0.121 0.870 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (39 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 101: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -189236099 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.039 0.019 199.1 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 230.625 0.104 0.749 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (36 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 101: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to 1736375543 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.044 0.022 199.3 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 202.143 0.119 0.855 0.005 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (38 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 101: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -386801669 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.082 0.041 199.6 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 108.752 0.221 1.589 0.003 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (59 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 101: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -168297601 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.050 0.025 199.3 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 178.647 0.134 0.967 0.004 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (42 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 101: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -508870667 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.058 0.029 199.4 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 154.743 0.155 1.117 0.004 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (45 ms) 101: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 101: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 101: Rotation group 0 'system' has 4 atoms 101: Number of degrees of freedom in T-Coupling group rest is 9.00 101: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 101: 101: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 101: NVE simulation with an initial temperature of zero: will use a Verlet 101: buffer of 10%. Check your energy drift! 101: 101: Enforced rotation: group 0 has 4 reference positions. 101: Reading them from /build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/rotref.0.trr. 101: 101: There was 1 NOTE 101: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 101: Can not increase nstlist because an NVE ensemble is used 101: Using 1 MPI thread 101: Using 2 OpenMP threads 101: 101: 101: NOTE: The number of threads is not equal to the number of (logical) cpus 101: and the -pin option is set to auto: will not pin threads to cpus. 101: This can lead to significant performance degradation. 101: Consider using -pin on (and -pinoffset in case you run multiple jobs). 101: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 101: 25 steps, 0.1 ps. 101: Setting the LD random seed to -357237337 101: 101: Generated 1 of the 1 non-bonded parameter combinations 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonA' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonB' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonC' 101: 101: Excluding 1 bonded neighbours molecule type 'ArgonD' 101: 101: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon4.gro', all velocities are zero 101: 101: This run will generate roughly 0 Mb of data 101: 101: Writing final coordinates. 101: 101: Core t (s) Wall t (s) (%) 101: Time: 0.062 0.031 199.2 101: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 101: Performance: 144.408 0.166 1.197 0.003 101: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 101: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 101: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (49 ms) 101: [----------] 12 tests from RotationWorks/RotationTest (488 ms total) 101: 101: [----------] Global test environment tear-down 101: [==========] 12 tests from 1 test suite ran. (503 ms total) 101: [ PASSED ] 12 tests. 101/103 Test #101: MdrunRotationTests ........................ Passed 0.53 sec test 102 Start 102: MdrunSimulatorComparison 102: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" 102: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 102: Test timeout computed to be: 600 102: [==========] Running 94 tests from 4 test suites. 102: [----------] Global test environment set-up. 102: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 102: NVE simulation: will use the initial temperature of 68.810 K for 102: determining the Verlet buffer size 102: 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.110 0.055 199.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 26.785 0.896 3.226 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.040 0.020 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 72.255 0.332 1.196 0.010 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 102: 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (96 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 102: NVE simulation: will use the initial temperature of 68.810 K for 102: determining the Verlet buffer size 102: 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.043 0.022 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 68.221 0.352 1.266 0.009 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.039 0.020 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 74.268 0.323 1.163 0.010 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (60 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.036 0.018 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 81.216 0.296 1.064 0.011 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.029 0.014 198.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 101.971 0.235 0.847 0.014 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (52 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.053 0.027 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 54.999 0.436 1.571 0.008 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.015 0.007 197.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 196.391 0.122 0.440 0.027 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (55 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.553 0.276 199.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 5.315 4.516 16.257 0.001 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.034 0.017 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 84.966 0.282 1.017 0.012 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (313 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.046 0.023 199.5 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 64.145 0.374 1.347 0.009 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.031 0.015 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 94.778 0.253 0.912 0.013 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (57 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: 102: WARNING 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: 102: There were 2 WARNINGs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.039 0.019 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 75.707 0.317 1.141 0.011 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.028 0.014 198.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 102.755 0.234 0.841 0.014 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (52 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.040 0.020 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 72.969 0.329 1.184 0.010 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.030 0.015 198.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 98.671 0.243 0.876 0.014 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (53 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 102: MTTK coupling is deprecated and will soon be removed 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.037 0.019 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 78.436 0.306 1.102 0.011 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.033 0.016 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 89.484 0.268 0.966 0.012 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (53 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.034 0.017 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 86.629 0.277 0.997 0.012 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.018 0.009 198.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 165.199 0.145 0.523 0.023 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (45 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.037 0.019 197.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 78.449 0.306 1.101 0.011 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.025 0.012 198.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 118.241 0.203 0.731 0.016 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (50 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 102: MTTK coupling is deprecated and will soon be removed 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.044 0.022 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 66.606 0.360 1.297 0.009 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.027 0.014 198.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 107.430 0.223 0.804 0.015 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (55 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 102: Andersen temperature control methods assume nsttcouple = 1; there is no 102: need for larger nsttcouple > 1, since no global parameters are computed. 102: nsttcouple has been reset to 1 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.043 0.021 199.4 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 68.633 0.350 1.259 0.010 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.038 0.019 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 76.648 0.313 1.127 0.011 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (59 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 102: Andersen temperature control methods assume nsttcouple = 1; there is no 102: need for larger nsttcouple > 1, since no global parameters are computed. 102: nsttcouple has been reset to 1 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.052 0.026 199.5 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 56.377 0.426 1.533 0.008 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.022 0.011 198.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 129.650 0.185 0.666 0.018 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (56 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 102: Andersen temperature control methods assume nsttcouple = 1; there is no 102: need for larger nsttcouple > 1, since no global parameters are computed. 102: nsttcouple has been reset to 1 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.035 0.018 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 82.688 0.290 1.045 0.011 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.017 0.009 198.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 167.271 0.143 0.517 0.023 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (45 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 102: Center of mass removal not necessary for Andersen. All velocities of 102: coupled groups are rerandomized periodically, so flying ice cube errors 102: will not occur. 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 102: Andersen temperature control methods assume nsttcouple = 1; there is no 102: need for larger nsttcouple > 1, since no global parameters are computed. 102: nsttcouple has been reset to 1 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.029 0.015 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 101.156 0.237 0.854 0.014 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.025 0.012 198.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 118.184 0.203 0.731 0.016 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (45 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 102: Center of mass removal not necessary for Andersen. All velocities of 102: coupled groups are rerandomized periodically, so flying ice cube errors 102: will not occur. 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 102: Andersen temperature control methods assume nsttcouple = 1; there is no 102: need for larger nsttcouple > 1, since no global parameters are computed. 102: nsttcouple has been reset to 1 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.029 0.015 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 100.760 0.238 0.857 0.014 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.036 0.018 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 82.165 0.292 1.052 0.011 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (51 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 102: Center of mass removal not necessary for Andersen. All velocities of 102: coupled groups are rerandomized periodically, so flying ice cube errors 102: will not occur. 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 102: Andersen temperature control methods assume nsttcouple = 1; there is no 102: need for larger nsttcouple > 1, since no global parameters are computed. 102: nsttcouple has been reset to 1 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.028 0.014 198.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 106.135 0.226 0.814 0.015 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.023 0.011 198.5 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 128.595 0.187 0.672 0.018 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (44 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 102: NVE simulation: will use the initial temperature of 398.997 K for 102: determining the Verlet buffer size 102: 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.095 0.047 199.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 31.010 0.774 2.786 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.043 0.021 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 68.336 0.351 1.264 0.012 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (1109 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 102: NVE simulation: will use the initial temperature of 398.997 K for 102: determining the Verlet buffer size 102: 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.096 0.048 199.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 30.527 0.786 2.830 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.045 0.023 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 65.063 0.369 1.328 0.011 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (1091 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.096 0.048 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 30.519 0.786 2.831 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.048 0.024 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 60.546 0.396 1.427 0.011 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (1092 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.100 0.050 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 29.407 0.816 2.938 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.045 0.022 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 65.632 0.366 1.316 0.011 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (1109 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.096 0.048 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 30.476 0.788 2.835 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.047 0.024 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 61.681 0.389 1.401 0.011 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (1104 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.101 0.051 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 29.083 0.825 2.971 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.017 0.009 197.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 169.391 0.142 0.510 0.029 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (1107 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: 102: WARNING 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: 102: There were 2 WARNINGs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.096 0.048 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 30.496 0.787 2.833 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.045 0.022 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 65.294 0.368 1.323 0.011 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (1108 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.102 0.051 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 28.809 0.833 2.999 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.048 0.024 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 60.677 0.396 1.424 0.011 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (1106 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.097 0.049 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 30.108 0.797 2.870 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.050 0.025 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 58.002 0.414 1.490 0.010 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (1110 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.095 0.047 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 30.989 0.774 2.788 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.052 0.026 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 55.759 0.430 1.550 0.010 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (1107 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 102: Andersen temperature control methods assume nsttcouple = 1; there is no 102: need for larger nsttcouple > 1, since no global parameters are computed. 102: nsttcouple has been reset to 1 102: 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.097 0.049 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 30.095 0.797 2.871 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.055 0.027 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 53.602 0.448 1.612 0.009 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (1108 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 102: Andersen temperature control methods assume nsttcouple = 1; there is no 102: need for larger nsttcouple > 1, since no global parameters are computed. 102: nsttcouple has been reset to 1 102: 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.097 0.049 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 30.166 0.796 2.864 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.047 0.024 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 61.983 0.387 1.394 0.011 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (1115 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 102: Andersen temperature control methods assume nsttcouple = 1; there is no 102: need for larger nsttcouple > 1, since no global parameters are computed. 102: nsttcouple has been reset to 1 102: 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.095 0.048 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 30.737 0.781 2.811 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.055 0.028 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 53.345 0.450 1.620 0.009 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (1094 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 102: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) 102: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (15624 ms total) 102: 102: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 102: NVE simulation: will use the initial temperature of 68.810 K for 102: determining the Verlet buffer size 102: 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.016 0.008 198.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 183.417 0.131 0.471 0.025 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.031 0.016 199.5 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 93.234 0.257 0.927 0.013 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (44 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 102: NVE simulation: will use the initial temperature of 68.810 K for 102: determining the Verlet buffer size 102: 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.106 0.053 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 27.575 0.870 3.133 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.087 0.044 199.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 33.579 0.715 2.573 0.005 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (118 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 102: NVE simulation: will use the initial temperature of 68.810 K for 102: determining the Verlet buffer size 102: 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.095 0.047 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 30.990 0.774 2.788 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.089 0.045 199.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 32.853 0.731 2.630 0.005 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (114 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.110 0.055 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 26.581 0.903 3.250 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.082 0.041 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 35.631 0.674 2.425 0.005 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (117 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.129 0.065 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 22.667 1.059 3.812 0.003 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.145 0.073 199.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 20.187 1.189 4.280 0.003 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (159 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.106 0.053 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 27.760 0.865 3.112 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.086 0.043 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 34.255 0.701 2.522 0.005 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (119 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.123 0.062 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 23.869 1.005 3.620 0.003 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.078 0.039 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 37.472 0.640 2.306 0.005 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (130 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.105 0.053 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 27.912 0.860 3.095 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.089 0.045 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 32.824 0.731 2.632 0.005 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (118 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.107 0.053 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 27.537 0.872 3.138 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.088 0.044 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 33.148 0.724 2.606 0.005 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (119 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: 102: WARNING 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: 102: There were 2 WARNINGs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.094 0.047 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 31.336 0.766 2.757 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.086 0.043 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 34.070 0.704 2.536 0.005 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (112 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There was 1 NOTE 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.168 0.084 199.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 17.434 1.377 4.956 0.002 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.088 0.044 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 33.498 0.716 2.579 0.005 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (156 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 102: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 102: 1 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.070 0.035 199.5 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 41.670 0.576 2.073 0.006 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.013 0.007 197.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 216.252 0.111 0.400 0.030 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (61 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 102: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 102: 1 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.031 0.015 198.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 94.866 0.253 0.911 0.013 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.028 0.014 198.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 104.892 0.229 0.824 0.015 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (48 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 102: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 102: 1 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.031 0.015 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 94.926 0.253 0.910 0.013 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.028 0.014 198.8 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 104.318 0.230 0.828 0.014 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (50 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 102: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 102: 1 102: 102: Number of degrees of freedom in T-Coupling group System is 33.00 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: Generated 1 of the 1 non-bonded parameter combinations 102: 102: Excluding 1 bonded neighbours molecule type 'Argon' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/argon12.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.041 0.021 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 70.847 0.339 1.220 0.010 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'Argon' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.027 0.013 198.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 109.588 0.219 0.788 0.015 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (55 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 102: NVE simulation: will use the initial temperature of 398.997 K for 102: determining the Verlet buffer size 102: 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.099 0.050 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 29.474 0.814 2.931 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.027 0.014 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 107.976 0.222 0.800 0.019 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (1110 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 102: NVE simulation: will use the initial temperature of 398.997 K for 102: determining the Verlet buffer size 102: 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.103 0.051 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 28.538 0.841 3.028 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.023 0.012 199.0 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 126.730 0.189 0.682 0.022 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (1115 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 102: NVE simulation: will use the initial temperature of 398.997 K for 102: determining the Verlet buffer size 102: 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.137 0.069 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 21.427 1.120 4.032 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.063 0.032 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 46.418 0.517 1.861 0.008 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (1147 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.110 0.055 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 26.665 0.900 3.240 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.023 0.011 198.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 129.126 0.186 0.669 0.022 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (1122 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.104 0.052 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 28.175 0.852 3.067 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.033 0.016 198.9 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 89.521 0.268 0.965 0.016 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (1118 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.108 0.054 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 27.255 0.881 3.170 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.037 0.019 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 78.532 0.306 1.100 0.014 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (1121 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.100 0.050 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 29.428 0.816 2.936 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.057 0.028 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 51.609 0.465 1.674 0.009 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (1109 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.104 0.052 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 28.297 0.848 3.053 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.057 0.029 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 50.917 0.471 1.697 0.009 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (1116 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.127 0.064 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 23.022 1.042 3.753 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.051 0.026 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 57.400 0.418 1.505 0.010 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (1130 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: 102: WARNING 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: 102: There were 2 WARNINGs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.120 0.060 199.7 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 24.483 0.980 3.529 0.004 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.057 0.029 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 51.179 0.469 1.688 0.009 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (1123 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 102: The Berendsen thermostat does not generate the correct kinetic energy 102: distribution, and should not be used for new production simulations (in 102: our opinion). We would recommend the V-rescale thermostat. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 2 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.098 0.049 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 29.958 0.801 2.884 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.055 0.028 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 53.304 0.450 1.621 0.009 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (1114 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 102: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 102: 1 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.047 0.024 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 62.491 0.384 1.383 0.011 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.063 0.032 199.5 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 46.183 0.520 1.871 0.008 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (1091 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 102: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 102: 1 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.109 0.054 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 27.000 0.889 3.200 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.061 0.031 199.2 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 47.585 0.504 1.816 0.008 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (1117 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 102: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 102: 1 102: 102: 102: WARNING 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 102: The Berendsen barostat does not generate any strictly correct ensemble, 102: and should not be used for new production simulations (in our opinion). 102: We recommend using the C-rescale barostat instead. 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: 102: There was 1 WARNING 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.107 0.053 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 27.466 0.874 3.146 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.034 0.017 199.1 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 85.855 0.280 1.006 0.015 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (1117 ms) 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 102: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 102: 1 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Number of degrees of freedom in T-Coupling group System is 27.00 102: 102: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 102: You are using a plain Coulomb cut-off, which might produce artifacts. 102: You might want to consider using PME electrostatics. 102: 102: 102: 102: There were 3 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 330891 of the 330891 non-bonded parameter combinations 102: 102: Generated 330891 of the 330891 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/tip3p5.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.104 0.052 199.6 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 28.150 0.853 3.069 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 102: 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.059 0.030 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 49.471 0.485 1.746 0.009 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (1110 ms) 102: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (18298 ms total) 102: 102: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest 102: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Pull group 1 'FirstWaterMolecule' has 3 atoms 102: Pull group 2 'SecondWaterMolecule' has 3 atoms 102: Number of degrees of freedom in T-Coupling group System is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 102: NVE simulation: will use the initial temperature of 2573.591 K for 102: determining the Verlet buffer size 102: 102: Pull group natoms pbc atom distance at start reference at t=0 102: 1 3 2 102: 2 3 5 1.112 nm 1.000 nm 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 3 of the 3 non-bonded parameter combinations 102: 102: Generated 3 of the 3 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.042 0.021 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 69.143 0.347 1.250 0.005 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.058 0.029 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 50.523 0.475 1.710 0.004 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (74 ms) 102: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (74 ms total) 102: 102: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest 102: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 102: 102: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 102: Setting nstcalcenergy (100) equal to nstenergy (4) 102: 102: Generating 1-4 interactions: fudge = 0.5 102: Pull group 1 'FirstWaterMolecule' has 3 atoms 102: Pull group 2 'SecondWaterMolecule' has 3 atoms 102: Number of degrees of freedom in T-Coupling group System is 9.00 102: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 102: 102: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 102: NVE simulation: will use the initial temperature of 2573.591 K for 102: determining the Verlet buffer size 102: 102: Pull group natoms pbc atom distance at start reference at t=0 102: 1 3 2 102: 2 3 5 1.112 nm 1.000 nm 102: 102: There were 2 NOTEs 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: Generated 3 of the 3 non-bonded parameter combinations 102: 102: Generated 3 of the 3 1-4 parameter combinations 102: 102: Excluding 2 bonded neighbours molecule type 'SOL' 102: 102: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/spc2.gro' 102: 102: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 102: 102: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 102: 102: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 102: 102: Note that mdrun will redetermine rlist based on the actual pair-list setup 102: 102: This run will generate roughly 0 Mb of data 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.061 0.031 199.3 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 48.135 0.499 1.795 0.003 102: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 102: Can not increase nstlist because an NVE ensemble is used 102: Using 1 MPI thread 102: Using 2 OpenMP threads 102: 102: 102: You are using the following feature(s) which are partially, but not fully validated. Please check your results. If you find issues, report them on the GROMACS forum or at https://gitlab.com/gromacs/gromacs/-/issues 102: modular simulator with an integrator other than VV 102: 102: NOTE: The number of threads is not equal to the number of (logical) cpus 102: and the -pin option is set to auto: will not pin threads to cpus. 102: This can lead to significant performance degradation. 102: Consider using -pin on (and -pinoffset in case you run multiple jobs). 102: starting mdrun 'spc2' 102: 16 steps, 0.0 ps. 102: 102: Writing final coordinates. 102: 102: Core t (s) Wall t (s) (%) 102: Time: 0.052 0.026 199.5 102: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 102: Performance: 56.061 0.428 1.541 0.004 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 102: Opened /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 102: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 102: 102: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (78 ms) 102: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (78 ms total) 102: 102: [----------] Global test environment tear-down 102: [==========] 94 tests from 4 test suites ran. (34139 ms total) 102: [ PASSED ] 94 tests. 102/103 Test #102: MdrunSimulatorComparison .................. Passed 34.17 sec test 103 Start 103: MdrunVirtualSiteTests 103: Test command: /build/reproducible-path/gromacs-2026.2/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2026.2/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" 103: Working Directory: /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests 103: Test timeout computed to be: 600 103: [==========] Running 37 tests from 2 test suites. 103: [----------] Global test environment set-up. 103: [----------] 1 test from VirtualSiteVelocityTest 103: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 103: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 103: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 103: 103: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 103: NVE simulation with an initial temperature of zero: will use a Verlet 103: buffer of 10%. Check your energy drift! 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: 103: Dynamic load balancing report: 103: DLB was off during the run due to low measured imbalance. 103: Average load imbalance: 6.7%. 103: The balanceable part of the MD step is 44%, load imbalance is computed from this. 103: Part of the total run time spent waiting due to load imbalance: 3.0%. 103: 103: 103: NOTE: 48 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.072 0.036 199.3 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 21.388 1.122 4.040 0.006 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: trr version: GMX_trn_file (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (60 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 103: NVE simulation with an initial temperature of zero: will use a Verlet 103: buffer of 10%. Check your energy drift! 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: 103: Dynamic load balancing report: 103: DLB was off during the run due to low measured imbalance. 103: Average load imbalance: 6.8%. 103: The balanceable part of the MD step is 45%, load imbalance is computed from this. 103: Part of the total run time spent waiting due to load imbalance: 3.0%. 103: 103: 103: NOTE: 48 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.055 0.028 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 28.083 0.855 3.077 0.008 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (49 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 103: NVE simulation with an initial temperature of zero: will use a Verlet 103: buffer of 10%. Check your energy drift! 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: 103: Dynamic load balancing report: 103: DLB was off during the run due to low measured imbalance. 103: Average load imbalance: 6.8%. 103: The balanceable part of the MD step is 43%, load imbalance is computed from this. 103: Part of the total run time spent waiting due to load imbalance: 3.0%. 103: 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.030 0.015 198.2 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 51.632 0.465 1.673 0.014 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (33 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.034 0.017 198.5 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 46.016 0.522 1.878 0.013 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (49 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.041 0.021 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 37.579 0.639 2.299 0.010 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (54 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.036 0.018 198.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 43.462 0.552 1.988 0.012 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (50 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 4 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.035 0.018 198.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 43.610 0.550 1.981 0.012 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (50 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 4 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.037 0.019 198.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 41.311 0.581 2.091 0.011 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (51 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 103: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 103: 1 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 4 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 4 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.040 0.020 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 38.183 0.629 2.263 0.011 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (53 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 103: NVE simulation with an initial temperature of zero: will use a Verlet 103: buffer of 10%. Check your energy drift! 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: 103: Dynamic load balancing report: 103: DLB was off during the run due to low measured imbalance. 103: Average load imbalance: 6.6%. 103: The balanceable part of the MD step is 42%, load imbalance is computed from this. 103: Part of the total run time spent waiting due to load imbalance: 2.8%. 103: 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.049 0.025 199.0 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 31.531 0.761 2.740 0.009 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (43 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 103: NVE simulation with an initial temperature of zero: will use a Verlet 103: buffer of 10%. Check your energy drift! 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Can not increase nstlist because an NVE ensemble is used 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: 103: Dynamic load balancing report: 103: DLB was off during the run due to low measured imbalance. 103: Average load imbalance: 10.4%. 103: The balanceable part of the MD step is 48%, load imbalance is computed from this. 103: Part of the total run time spent waiting due to load imbalance: 5.0%. 103: 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.050 0.025 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 30.990 0.774 2.788 0.009 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (42 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 48 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.047 0.024 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 32.954 0.728 2.622 0.009 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (55 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.037 0.018 198.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 42.154 0.569 2.050 0.012 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (50 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.040 0.020 198.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 38.855 0.618 2.224 0.011 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (51 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.036 0.018 198.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 42.815 0.561 2.018 0.012 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (50 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.030 0.015 198.4 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 51.339 0.467 1.683 0.014 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (47 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.038 0.019 198.8 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 40.386 0.594 2.139 0.011 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (51 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Taking velocities from '/build/reproducible-path/gromacs-2026.2/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 46 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.031 0.016 198.6 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 49.328 0.487 1.752 0.014 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (47 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.043 0.022 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 35.809 0.670 2.413 0.010 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (66 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.039 0.019 198.9 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 39.937 0.601 2.163 0.011 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (64 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 103: 103: NOTE 1 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 103: Setting nstcalcenergy (100) equal to nstenergy (4) 103: 103: Number of degrees of freedom in T-Coupling group System is 45.00 103: 103: NOTE 2 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 103: There are 6 non-linear virtual site constructions. Their contribution to 103: the energy error is approximated. In most cases this does not affect the 103: error significantly. 103: 103: 103: NOTE 3 [file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 103: You are using a plain Coulomb cut-off, which might produce artifacts. 103: You might want to consider using PME electrostatics. 103: 103: 103: 103: There were 3 NOTEs 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 103: 103: Update groups can not be used for this system because an incompatible virtual site type is used 103: 103: Using 2 MPI threads 103: Using 1 OpenMP thread per tMPI thread 103: 103: 103: NOTE: The number of threads is not equal to the number of (logical) cpus 103: and the -pin option is set to auto: will not pin threads to cpus. 103: This can lead to significant performance degradation. 103: Consider using -pin on (and -pinoffset in case you run multiple jobs). 103: starting mdrun 'Virtual sites test system in vacuo' 103: 8 steps, 0.0 ps. 103: Generated 3 of the 6 non-bonded parameter combinations 103: 103: Excluding 3 bonded neighbours molecule type 'VSTEST' 103: 103: Cleaning up constraints and constant bonded interactions with virtual sites 103: 103: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 103: 103: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 103: 103: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 103: 103: Note that mdrun will redetermine rlist based on the actual pair-list setup 103: 103: This run will generate roughly 0 Mb of data 103: 103: Writing final coordinates. 103: 103: NOTE: 47 % of the run time was spent communicating energies, 103: you might want to increase some nst* mdp options 103: 103: Core t (s) Wall t (s) (%) 103: Time: 0.037 0.018 198.7 103: (ns/day) (hour/ns) (ms/step) (Matom*steps/s) 103: Performance: 42.070 0.570 2.054 0.012 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: Reading file /build/reproducible-path/gromacs-2026.2/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2026.2-Debian_2026.2_2 (double precision) 103: 103: Reading virtual site types... 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (63 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 103: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 103: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 103: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (1091 ms total) 103: 103: [----------] Global test environment tear-down 103: [==========] 37 tests from 2 test suites ran. (1107 ms total) 103: [ PASSED ] 37 tests. 103/103 Test #103: MdrunVirtualSiteTests ..................... Passed 1.14 sec The following tests passed: GmxapiExternalInterfaceTests GmxapiInternalInterfaceTests NbLibListedForcesTests NbLibSamplesTestArgon NbLibSamplesTestMethaneWater NbLibUtilTests NbLibSetupTests NbLibTprTests NbLibIntegrationTests NbLibIntegratorTests threadMPI-mpithreads threadMPI-sync_cyclecount threadMPI-mpi_speedtest threadMPI-notmpi threadMPI-alloc_check TestUtilsUnitTests TestUtilsMpiUnitTests UtilityUnitTests MpiCommTests UtilityMpiUnitTests AwhTest DensityFittingAppliedForcesUnitTest QMMMAppliedForcesUnitTest ColvarsAppliedForcesUnitTest PlumedAppliedForcesUnitTests PlumedMDTests NNPotAppliedForcesUnitTest AppliedForcesUnitTest ListedForcesTest NbnxmTests NbnxmGpuTests GmxlibTests GmxlibGpuTests CommandLineUnitTests DomDecTests DomDecMpiTests EwaldUnitTests FFTUnitTests FmmInterfaceUnitTests GpuUtilsUnitTests GpuUtilsMpiTests HardwareUnitTests MathUnitTests MdrunUtilityUnitTests MdrunUtilityMpiUnitTests MDSpanTests MdtypesUnitTest OnlineHelpUnitTests OptionsUnitTests PbcutilUnitTest RandomUnitTests RestraintTests SerializationUnitTests TableUnitTests TaskAssignmentUnitTests GmxTimingTests TopologyTest PullTest SimdUnitTests CompatibilityHelpersTests GmxAnaTest GmxPreprocessTests Pdb2gmx1Test Pdb2gmx2Test Pdb2gmx3Test CorrelationsTest AnalysisDataUnitTests CoordinateIOTests TrajectoryAnalysisUnitTests EnergyAnalysisUnitTests ToolUnitTests ToolWithLeaksUnitTests H5mdTests FileIOTests SelectionUnitTests MdrunOutputTests MdrunModulesTests MdrunIOTests MdrunTestsOneRank MdrunTestsTwoRanks MdrunSingleRankAlgorithmsTests Minimize1RankTests Minimize2RankTests MdrunNonIntegratorTests MdrunTpiTests MdrunMpiTests MdrunMultiSimTests MdrunMultiSimReplexTests MdrunMultiSimReplexEquivalenceTests MdrunMpi1RankPmeTests MdrunMpi2RankPmeTests MdrunMpi4RankPmeTests MdrunCoordinationBasicTests1Rank MdrunCoordinationBasicTests2Ranks MdrunCoordinationCouplingTests1Rank MdrunCoordinationCouplingTests2Ranks MdrunCoordinationConstraintsTests1Rank MdrunCoordinationConstraintsTests2Ranks MdrunFEPTests MdrunPullTests MdrunRotationTests MdrunSimulatorComparison MdrunVirtualSiteTests 100% tests passed, 0 tests failed out of 103 Label Time Summary: GTest = 975.36 sec*proc (96 tests) IntegrationTest = 648.54 sec*proc (30 tests) MpiTest = 738.56 sec*proc (24 tests) QuickGpuTest = 156.92 sec*proc (24 tests) SlowGpuTest = 751.57 sec*proc (15 tests) SlowTest = 318.37 sec*proc (14 tests) UnitTest = 8.45 sec*proc (52 tests) Total Test time (real) = 468.40 sec touch build-basic dh_testdir LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2026.2/build/mpi/lib /usr/bin/make -j4 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2026.2/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2026.2 -B/build/reproducible-path/gromacs-2026.2/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2026.2/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2026.2/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/selection /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" scanner make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/external/rpc_xdr /build/reproducible-path/gromacs-2026.2/build/mpi/src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/DependInfo.cmake "--color=" internal_rpc_xdr make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" thread_mpi make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build /usr/bin/make -f src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build.make src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/parser.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr/xdr.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2026.2-Debian_2026.2_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2026.2 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.2/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2026.2/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2026.2-2 -P /build/reproducible-path/gromacs-2026.2/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/selection/scanner.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_array.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr/xdr_array.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_float.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr/xdr_float.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/external/rpc_xdr && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/external/rpc_xdr/CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -MF CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o.d -o CMakeFiles/internal_rpc_xdr.dir/xdr_stdio.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/rpc_xdr/xdr_stdio.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 0%] Built target internal_rpc_xdr /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" tng_io_obj make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/bwlzh.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 0%] Built target thread_mpi /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" lmfit_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/lmfit/lmmin.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/coder.c /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvar.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/dict.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF 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/usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o 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/build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/compression/xtc3.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 0%] Built target scanner cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias.cpp /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fmm /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fmm/CMakeFiles/fmm.dir/DependInfo.cmake "--color=" fmm make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/fmm/CMakeFiles/fmm.dir/build.make src/gromacs/fmm/CMakeFiles/fmm.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdmodule.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmm_mdmodule.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmm_mdpoptions.cpp /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -DGMX_DESCRIBE_BLAS="External - detected on the system" -DGMX_DESCRIBE_LAPACK="External - detected on the system" -DGMX_FFT_MKL=0 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/binary_information.cpp.o -MF CMakeFiles/linearalgebra.dir/binary_information.cpp.o.d -o CMakeFiles/linearalgebra.dir/binary_information.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/binary_information.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/eigensolver.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -MF CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o.d -o CMakeFiles/fmm.dir/fmm_mdpvalidator.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmm_mdpvalidator.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2026.2/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -MF CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceproviderbuilder.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmmforceproviderbuilder.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 3%] Built target tng_io_obj cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmoptions.cpp.o -MF CMakeFiles/fmm.dir/fmmoptions.cpp.o.d -o CMakeFiles/fmm.dir/fmmoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmmoptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abmd.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_abmd.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 5%] Built target linearalgebra cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fmm && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fmm/CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -MF CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o.d -o CMakeFiles/fmm.dir/fmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fmm/fmmforceprovider_stub.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/options /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" options make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/abstractoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 5%] Built target fmm cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_histogram.cpp /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" pulling make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pull_rotation.cpp /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fileio/h5md /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/DependInfo.cmake "--color=" h5md make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build.make src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/fileio/h5md && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/fileio/h5md/CMakeFiles/h5md.dir/h5md.cpp.o -MF CMakeFiles/h5md.dir/h5md.cpp.o.d -o CMakeFiles/h5md.dir/h5md.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/fileio/h5md/h5md.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 5%] Built target h5md cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/filenameoptionmanager.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/programs /build/reproducible-path/gromacs-2026.2/build/mpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/pullutil.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 5%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/optionsassigner.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/programs /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/programs /build/reproducible-path/gromacs-2026.2/build/mpi/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_opes.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_opes.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 5%] Built target pulling cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarbias_restraint.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/timeunitmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 5%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/options/treesupport.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_alchlambda.cpp [ 7%] Built target options /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" energyanalysis make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/energyanalysis && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/energyanalysis/energyterm.cpp /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" taskassignment make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/decidegpuusage.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 7%] Built target energyanalysis cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/findallgputasks.cpp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.2/build/mpi /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" modularsimulator make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include 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src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarcomp_neuralnetwork.cpp 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -MF CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o.d -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator/statepropagatordata.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include 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CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_colvar.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarscript_commands_colvar.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/colvarvalue.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -Wno-old-style-cast -Wno-cast-qual -Wno-suggest-override -Wno-suggest-destructor-override -Wno-zero-as-null-pointer-constant -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 12%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2026.2/build/mpi' [ 14%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2026.2/build/mpi' cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2026.2/build/mpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2026.2/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2026.2 /build/reproducible-path/gromacs-2026.2/src/gromacs /build/reproducible-path/gromacs-2026.2/build/mpi 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/build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 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-I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2026.2/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2026.2/build/mpi/src/gromacs && /usr/bin/mpicxx -DCOLVARS_MPI -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2026.2/src/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/src/include -I/build/reproducible-path/gromacs-2026.2/src -I/build/reproducible-path/gromacs-2026.2/src/external/tng_io/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem 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-I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2026.2/src/external -isystem /build/reproducible-path/gromacs-2026.2/src/gromacs/../external/rpc_xdr -isystem /build/reproducible-path/gromacs-2026.2/src/external/lmfit -isystem /build/reproducible-path/gromacs-2026.2/src/external/colvars -isystem /build/reproducible-path/gromacs-2026.2/src/external/plumed -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2026.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC 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-I/build/reproducible-path/gromacs-2026.2/build/mpi/tng/include -I/build/reproducible-path/gromacs-2026.2/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/math/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/serialization/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2026.2/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2026.2/src/external/thread_mpi/include -isystem 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